1 2These changes are always immediately updated in the "molden5.x.tar.Z" 3source file, however the platform dependent executables in the 4directory "/pub/molgraph/molden/bin" on the ftp site are not always 5in tune with the latest changes, check the date on the executable. 6 7------------------------------------------------------------------------ 8 9molden5.8.2 10 11Tue Aug 14 12- Docking was introduced in molden5.8, but this code did not always 13 yield the same results on the docking tests in the test/dock directory. 14 This in contrast to results on my development machine. 15 molden5.8.2 fixes some of these issues. 16 17molden5.8.1 18 19Fri Aug 3 20 21- Made some adjustments to the C code (xwin.c) to make it compile 22 better on MacOSX 23 24Thu Jul 26 25 26- This version of molden, the electron density files for proteins are 27 obtained from a different site. The old one: the Electron Density 28 Server in Sweden is being phased out. Now we have to obtain electron 29 density files from www.ebi.ac.uk/pdbe. However the old site used 30 amongst others the BRICK/OMAP format of density files. The new site uses 31 the CCP4 format of density files. These are stream files, generated 32 by C programs. Fortran 2003 can read stream files, but some older 33 versions of fortran can not (f77,g77). These version of compilers 34 will generate errors. 35 36- Heikki Tuononen reported a bug in molden5.8 with writing xyz files from 37 the Z-matrix editor. 38 39- Also on recommendation of Heikki Tuononen we incorporated tables of 40 bond radii based Pyykkö's and Atsumi's values. 41 http://www.chem.helsinki.fi/~pyykko/Radii09.pdf 42 43Molden5.8 44 45 46Wed May 23 2018 47 48- Three main functionalities were added in the molden5.8 release: 49 50 - molecular docking 51 - the updating of the nwchem functionality 52 - the writing of lammps input files from an ambfor .xyz file 53 by the ambfor executable by usage of the -l keyword 54 55 Molecular Docking 56 57 The docking functionality is a hybrid scheme of the FlexX docking 58 and a force field (amber+gaff) optimisation. 59 The same scheme as meployed by FlexX was used to generate the placement 60 of the base fragment. So first distance tables are generated to store 61 all the distances between the interaction points in the protein. 62 The protein has to be supplied in a pdb format with hydrogens present. 63 Molden can be used to generate such a pdb file. For now, the orientation 64 of for example OH groups (Serine,Threonine,tyrosine) have to be predefined. 65 The user can define a sphere around a to be picked point, which encloses 66 all the interaction points which are relevant for the docking. 67 These interaction point can be either H(ydrogen Bond)_Acc(eptor), 68 H(ydrogen Bond)_Don(onor) or aromatic/ch(2,3). The user selected 69 amino acid residues are then assigned interaction points. 70 For each combination of interaction groups, distances are collected and 71 stored in a distance table. 72 Next a ligand must be supplied in ambfor .xyz format (molden own force 73 field format), also charges must have been assigned for proper force 74 field scoring. 75 Next interaction points are assigned to the ligand. From these interaction 76 triples are generated. This list of triples is searched against the distance 77 tables to find matching protein interaction triples, 78 these are called base fragment 79 For the ligand two to three interaction points are generate for each 80 OH group. 81 Initially the ligand is divident up into fragments. Fragments are typically 82 connected by single SP3-SP3 or SP2-SP3 bonds. These fragments are stored 83 internally by molden. This fragmentation is used to generate different 84 conformations of the ligand by rotating around the dihedral angles of the 85 single bonds separating the fragments. The bonds that are not strict 86 SP2-SP3 bonds are kept in order to carry out a complete scan of the energy 87 with respect to these dihedrals. For regular SP3-SP3 bonds the standard 88 angles of the staggered conformations of ethane are employed. 89 When the debug button is pressed in the "Docking Start" window a file 90 called "conformers.mol2" is written. 91 The orientation of the base fragment is very important for the following 92 steps in the docking procedure. That is why the base fragment placement is 93 optimised to obtain a near perfect placement. If we had a base fragment 94 consisting of all Hydrogen bond acceptors and donors, the van der waals 95 part of the force field scoring is reduced, so that the orientation is 96 dominated by electrostatic part of the force field scoring. 97 If we were dealing with a base fragment with one pair of Hydrogen bond 98 acceptors or donors and one hydrophobic interaction point, we rotate 99 around the axis formed by pair to find the energetically optimal angle for 100 the remaining hydrophobic interaction point with respect to the pair. 101 Because the hydrophobic interaction between hydrophobic interaction points 102 are much smaller than between a acceptor and donor pair (round about 103 seven times weaker) and are much less well defined in space, the optimal 104 placement is rarely the one found in the original base placement, but 105 will be impacted more by the rest of the ligands placement. 106 The main scheme assumes a base fragment that has 107 interaction points belonging to the same fragment. This is by far the 108 fastest docking scheme. Here we map the base fragment onto the earlier 109 created conformers (Debug: mconformers.mol2), followed by an optimisation 110 of the conformers along the dihedrals of the non-pure single bonds 111 that molden stored earlier. 112 However when a ligand triplet with two or more Hydrogen bond acceptor/donor 113 interaction points can not be formed from the same fragment, a different 114 docking scheme is employed. Now we use the whole of the conformations of the 115 ligand to sample ligand points, but to make the algoritm more efficient we 116 only keep the unique ones (unique by location of the interaction points 117 origin) and store the conformations it belongs to with these interaction 118 points. After optimisation of the base fragments, the ligand poses are 119 generated from the combined confomer information of the three interaction 120 points. If all three interaction points are from the same conformer, 121 this conformer is mapped onto the base fragment, followed by an optimisation 122 of the conformers along the dihedrals of the non-pure single bonds 123 that molden stored earlier. 124 The force field scoring is stored into the multi-mol result dock.mol2 125 file. 126 The source distribution of molden5.8 has a 'dock' subdirectory of the test 127 directory, with three different docking: 128 129 - ligand dtst.xyz (part of MTX) into the 4dfr protein. 130 (fastest: all three interaction points on the same fragment) 131 132 - ligand est.xyz into the 1a52 protein. 133 Slower because the default interaction point separation of 10 angstrom 134 has to be increased. 135 136 - ligand rsb.xyz (part of RAL(oxifen)) into the 1err protein. 137 (slowest: NOT all three interaction points on the same fragment) 138 139 This is the launching of a prototype that will undergo extensive testing 140 in the coming months. 141 142 CAVEATS/Missing functionality: 143 144 - the orientation of the for example OH groups (Serine,Threonine,tyrosine) 145 have to be predefined in the PDB file. 146 147 - Structural and Non-structural waters are ignored in the docking. 148 149 - Docking into an active site with metals is not yest supported. 150 151 - No ring conformations are being searched 152 153 154 155 Updated nwchem functionality 156 157 Molden NWCHEM functionality has been updated. Previous versions of 158 molden could not display orbitals or density from NWCHEM because the 159 required information was missing from the NWCHEM output. However 160 NWCHEM is bundled with the ecce program, this program can display 161 the orbitals and other properties by incorporating ecce_print 162 command into the nwchem input file. Molden can now also read these 163 ecce.out files. This opens up a lot of functionality compared to 164 that of only the nwchem output file information being available. 165 166 Some caveats: 167 168 The scf convergence information written to the ecce.out 169 is not correct. At least in the somewhat old combination 170 of ecce and nwchem we used (nwchem 6.3) 171 172 Molden can not correctly calculate esp charges when dummys 173 are being used 174 175 Beside the reading of ecce files, molden can now also submit nwchem jobs 176 via the z-matrix editor (use the NWCHEM button in the format section 177 followed by "Submit Job"). The command nwchem must be defined for this to 178 work correctly. 179 180 WRITING OF LAMMPS INPUT FILES 181 182 Large-scale Atomic/Molecular Massively Paralell Simulator (LAMMPS) 183 input files can be generated from an Ambfor .xyz file, by Molden 184 own force field helper programs ambfor by typing: 185 186 ambfor -s -l test.xyz 187 188 After this a file called 'gaff.lammps' will have been written. 189 190 MISCELLANEOUS 191 192 - The reading of molden format files (such as vib.molden) has been repaired 193 194 - When reading multi-mol file such as a .mol2 file contaning multiple 195 structures, followed by reading an other multi-mol file when still having 196 the multi-mol window open, would lead to adding the entries to the entries 197 already present from the previuos read. This has been fixed. 198 199 200Wed May 17 2017 201 202- This is mainly an update to deal with the in my view 'crazily' increased 203 strictness of the gcc 5.4 compiler. This compiler spews out a ridiculous 204 number of warning messages. To cope with this, proper function proto typing 205 was applied to xwin.c. (Language purists always give me the creeps !) 206 207 208Molden5.7 209 210 211- Gaussian 16 was not recognised, which led to improper processing 212 of Guassian16 output/log files. Updated rdgaus.f to deal with this. 213 214 215Thu Jan 26 2017 216 217- Adjusted the dropdown list to print "<- to top" at the end of long 218 lists, previously it would say "more ..". 219 220- gmolden: adding caps to proteins from the 'protein view' of the 221 z-matrix editor would effectively work, however the screen 222 was not updated. Fixed 223 224- The ambfor .xyz files offer the possibility of keeping some atoms fixed. 225 However, molden/gmolden did not transfer this info to the ambfor program. 226 Also, the ambfor program did not deal with these atoms correctly. Fixed 227 228Wed Sep 21 229 230- I have updated the auxiliary files in the plush directory, needed by 231 molden to add hydrogens to PDB ligands (HETATM 's). 232 I plan to do this each half year. 233 234- during this update problems appeared with specific PDB entries, of which 235 a number have been resolved: 236 237 Ligand 3TV in pdb entry 4wr7: 238 239 HIS 119 complexes with Zn, but had its H pointing towards positive Zn 240 241 242 Ligand 3VU in pdb entry 4wz4: 243 Ligand 3Y6 in pdb entry 4x6t: 244 245 COOH group deprotonated, charge should be -1, molden said 0 246 This caused by a boron with 4 connections in the ligand. 247 We created a isBH4() function, if it is BH4, nht is not decreased ! 248 249 250 Ligand 3XT in pdb entry 4x6h: 251 252 Ligands 3XT and I37 have overlapping coordinates and therefor 253 are interconnected ! So the number of connections do NOT correspond to 254 that of the plush 3XT file !!! Causing molden not to add the hydrogens 255 and print: 256 257 Decreasing formal charge by -38 units !!!!!!! 258 259 We now check for overlapping ligands and alert the user. 260 261 262 Ligand 3XZ in pdb entry 4tys: 263 264 Molden has a routine for adding a Hydrogen to a tertiary nitrogen 265 on a ligand. However in this case it puts a Hydrogen on a tertiary 266 nitrogen in a flat 5 membered ring, so the N should have a sp2 267 268 269 Ligand 3YO in pdb entry 4rx5: 270 271 The plush file for 3YO had one Hydrogen specified in the pdb file: 272 273 HETATM 2322 H27 3YO A 706 -34.242 29.736 -8.804 1.00 15.26 274 275 This is very unusual. 276 Just let molden add the other. 277 278 Ligand 1WD in pdb entry 4yw8: 279 280 1WD coordiates with an Mn, Lys 244 also coordinates with the Mn, 281 there one H of the lys should be removed. We already have this 282 functionality for HIS residues, now we added it for lys. 283 We had to increase the van der Waals radius of Mn a tiny bit to 284 get this right. 285 286Fri Aug 12 287 288- Added the possibility of editable text fields to be longer than the visible 289 string. Now for example file names can be 1024 charachters long. 290 The visible (and editable) part of the string is a movable window on top 291 of the whole string. When you get to the edges of the string (using the 292 left and right arrow keys) the windows position will move up or down one 293 position with respect to the whole string. 294 295- Concerns only protein PDB files: 296 297 Molden already had the ability to pop up a window with commands, when 298 clicking with the second mouse button on a residue on screen. 299 Now I have added a "select range" command to this window. This will let 300 the user select a range of amino acids, starting from the amino acid 301 just clicked on, moving up or down in residue number, following the tip of 302 the red arrow on screen. The selection is ended by hitting the escape key. 303 304- Particulary the first option required a lot of changes to the code and 305 there are bound to be some problems to be ironed out ! 306 Hence the version of molden. 307 308Molden5.6 309 310Sun jul 24 311 312- The Mac OSX version had the problem that it did not load the OMAP 313 electron density file for proteins. Fixed now. (not in the .dmg file) 314 315Wed jul 20 316 317- I found out that the displaying of the electron density ontop of a 318 protein (pdb file), only really worked for cells with three angles 319 of 90 degrees. I now have adapted the program to also deal with maps 320 where one angle is not 90 (this at least covers the most abundant 321 spacegroup in the PDB databank). I still have to work on triclinic 322 spacegroups. 323 324- Fixed problem with clipping protein surfaces, now the clipping is 325 independent of the amount of zoom. Also the clipping did not cover 326 the whole protein surface. Fixed it. 327 328- Fixed the annoying problem that a window which you swiped your mouse over 329 to reach the window of interest pops up help on a button, making the 330 window you are currently working on unresponsive. 331 (Does NOT yet work for the windows version of gmolden). 332 333Fri Jun 24 334 335- removed a bug introduced with the reading file in memory functionality. 336 When optimising a structure in the background, after reading a pdb file 337 the reading routines were still in memfil mode, this caused problems. 338 Fixed it. 339 340- when reading files that contain multiple structures when opening the 341 z-matrix editor the z-matrix of the first structure was always displayed. 342 Now the z-matrix of the selected structure is displayed. 343 344Thu Jun 23 345 346- Provided binaray distributions containing besides 347 molden,gmolden,ambfor,ambdm,surf the pharmer and obabel executables. 348 349 pharmer has to be ported to windows, which was no easy feat. 350 351 You can find the binary distributions under the following URL's: 352 353 Linux ubuntu 32 bits: 354 355 ftp://ftp.cmbi.umcn.nl/pub/molgraph/molden/bin/Linux/molden5.6.full.ubuntu.32.tar.gz 356 357 Linux ubuntu 64 bits: 358 359 ftp://ftp.cmbi.umcn.nl/pub/molgraph/molden/bin/Linux/molden5.6.full.ubuntu.64.tar.gz 360 361 Windows (32 bits): 362 363 ftp://ftp.cmbi.umcn.nl/pub/molgraph/molden/bin/Windows/molden_native_windows_full.rar 364 365 MacOSX (64 bits)*: 366 367 ftp://ftp.cmbi.umcn.nl/pub/molgraph/molden/bin/MacOSX/molden5.6_MacOSX_full.tar.gz 368 369 370 *) you may need to install 'wget' to be able to download pdb files from the 371 file browser. Install home brew for Mac and install wget: 372 brew install wget 373 *) This version was installed on El Capitan with the latest gfortran 374 version it contains all necessary libraries and may therefor also run 375 on older MacOSX iterations. 376 377- Fixes a bug in calculating the electron density from the EDS protein 378 crystallograpy server files. 379 380- Fixes a bug that would result in molden not displaying all H positions correct 381 when generating rotamers from a PDB file generated by the MOE program. 382 383- Uses fork instead of vfork on MacOSX: now a molecule will optimise in the 384 background also on Mac OSX. 385 386Wed May 18 387 388- fixed a bug introduced in molden5.4. 389 With a zmatrix created for an pdb file, the dihedral for rotation 390 of the OH/SH was missing from the protein view of the z-matrix 391 Also in the full atom mode of the z-matrix the corresponding dihedral 392 was not behaving properly. 393 394Wed May 11 395 396- Added an interface to the fingerprint searching capabilities of openbabel. 397 Openbabel version 2.3.0 or higher is required (URL: openbabel.org). 398 When reading in a .sdf file from the file selector 399 (NOT from the command line!), molden will check if the obabel executable 400 is available (in /usr/local/bin). If it is there it will try to generate 401 a 2D (SVG) representation for each molecule in the .sdf file and display 402 them in the multi-mol listbox. 403 This is accomplished via a background process. When it is finished, it will 404 write out the 2D representations with the original file name of the .sdf 405 file, but now with extension .svgs 406 The next time you read in this .sdf file molden will first look for the 407 .svgs file and read it in. 408 409 When the obabel executable is found molden will add two extra buttons 410 to the "Multi-mol file" window: 411 412 . "create fingerprint index" will use obabel to create a fast searching index 413 of this .sdf file (with the same file name but with the .fs extension). 414 415 . Clicking "Search" will add a few query boxes to the "Multi-mol file" 416 window. The query file must be one of the formats supported by openbabel. 417 (.mol file will work). The query is searched against the fast searching 418 index of the .sdf file. Entries from the original .sdf file with a tanimoto 419 coefficient greater than the value supplied by the user (0.6 default), will 420 be stored int the results .sdf file (default res.sdf). 421 422- Added an interface to the pharmacophore searching capabilities of pharmer. 423 Pharmer is an open source program developed by David Koes. 424 Pharmer powers ZINCPharmer, an online pharmacophore search engine for a 425 multi-conformer library of the ZINC database. 426 427 Because pharmer is a nightmare to install, precompiled versions 428 (32 and 64 bits) will be supplied together with the binary distribution 429 of molden5.6 for ubuntu (openbabel will also be included). 430 431 When the pharmer executable is found (default /usr/local/bin) the option 432 "Pharmacophore Editor" will become available from the "Surface" icon 433 (7th from the top of the central icon column). 434 435 This will run pharmer to create the annotation of your molecule. 436 That is it will create a list of features for you to choose from 437 that you think is essential for interaction with the target protein. 438 439 From the pharmacophore Editor window you will be able to add features by 440 clicking the "Create" button, after you have first clicked the feature in 441 molecule display. A selected feature stores the associated coordinates, 442 you can then select other features available in the annotation for these 443 coordinates. (sometimes multiple features are available with the same 444 coordinates eg: aromatic and hydrophobic). You can also adjust the radius, 445 which defines a tolerance sphere around the feature. 446 447 When you are done with selecting features you can save the selection 448 by clicking the "Save" button. You can also restore previous selections 449 by clicking the "Open" button. Selections are stored in the json format. 450 451 When you click "Search" will open the "Pharmacophore Search Database" 452 window. This allows you to select a .sdf database file (Open button) 453 You can then create a Pharmer Database (index) by clicking 454 "Create DB Index". This will create a directory with the same directory 455 name as the original filename of the .sdf file, but with the .db extension. 456 457 Finally, clicking the "Search" button will search the Pharmer database 458 with the stored .json query and return the results in the .sdf file specified 459 in the "Results:" query box (default: phrm.sdf) 460 461 462Molden5.5 463 464Wed Apr 6 465 466- The routine that parses strings from files read in memory expected 467 strings no longer than 137 characters. Sometimes .sdf files contain 468 much longer lines. This would make molden crash. Fixed it. 469 470- PDB files written by MOE would contain an label unknown to molden ('HC") 471 Molden can now handle it. 472 473Thu Mar 8 474 475- Fixed the option ADD file for .mol2 file added to a PDB file. 476 477- Added the ADD file option to ADD .sdf file to a PDB file 478 Both these options are handy for looking at docking results, stored in 479 a .mol2 file or a .sdf file. 480 481- when having multiple structures, selecting one in the upper listbox 482 of the "structures" windows and ONE in the LOWER listbox; 483 the LOWER listbox could give problems with the scrolling. Solved by 484 making the listbox 4 entries deep in stead of 3. 485 486Thu Mar 3 487 488- In the PDB HETATM records there are sugar like compounds that can make 489 connections to other sugar HETATM records, often the connecting atom would 490 be an C-OH which after connecting would miss one hydrogen. 491 Fixed this by adding a NOTH field is the HETATM files in the plush 492 directory. The plush files contain information on the number of Hydrogens 493 attached to the non hydrogen atoms. 494 495- Some sugars connect to an ASN residue, often there would still be two 496 hydrogens on the C=ONH2 part plus the connection to the HETATM sugar. 497 Fixed this. 498 499Fri Feb 26 500 501- A number of bug fixes: 502 503 In the "Residue command" windows, typing eg: 1-40:A would also 504 erroneously activate waters. Fixed 505 506 PDB entry 471d: choosing optimise waters would lead to a neverending loop. 507 Fixed. 508 509 PDB entry 3jaa: would have wrong secundary structure connections on DNA 510 511 Reading a PDB file from the file manager, now reads the file into memory. 512 We hoped this would spead up the parsing of PDB files, however the speed up 513 was dissappointing. 514 515Fri Feb 5 516 517- bug fix: 518 519 When reading in two pdb structures, do backbone on the second, 520 delete active structure. When reading in the next pdb sturcture 521 and doing backbone, the helix, beta and coil were not visible. 522 523- A lot of minor bug fixes pertaining to PDB HETATM structures parsing: 524 525 pdb entry 4phg: HETATM 2UH makes connection to CYS, to connecting C atom 526 had no Hydrogens attached. 527 528 pdb entry 3c0g,4w9l,4w9k,4w9o,4w9p and probably more: 529 There two HETATM molecules with the same name and 530 same number. They were treated as one big molecule. 531 Now we also read the chain identifier, and now they are 532 treated as different residues. 533 534 pdb entry 3qn6, 4ylk and probably more: 535 HETATM molecule 3QN makes covalent bond with ASN259, 536 forming a petide bond: the hydrogen connected to the N 537 was pointing in the wrong direction. The fix makes the H ly 538 in a plane with N,C,C=O 539 540 HETATM PRX the hydrogens were not correctly added. 541 542Mon Jan 25 543 544- Removed a few small bugs that would cause problems with reading 545 fdat files, and gamess-uk output. 546 547Fri Jan 22 548 549- Adapted the molden code so that it can now read files in to memory. 550 More correctly: in can do the old fortran reading and reading of files 551 in memory, side by side. 552 Currently, this is only done for files with the .sdf extension. 553 This was done, to address the fact that reading large .sdf files was 554 extremely slow and a max. of 100 entries would be stored. 555 The reading of .sdf files is now completely dynamic, you can read any 556 .sdf files no matter how many entries it contains. That is to say, untill 557 your memory runs out :-) 558 This only works from within the file manager, NOT from the command line. 559 560 NOTE: This is all very new and errors are to be expected in the beginning. 561 562- Support for reading in charges from the pubchem.sdf files. 563 564 565End Molden5.4 566 567Tue Jan 5 568 569- Fixed a bug in the routine reading mopac .aux files. This could cause 570 some atoms to have exponents with a zero value. 571 572Fri Dec 11 573 574- added a born shell script register_extension.sh, to be run from the makefile 575 or by hand, which links gmolden to a number of file extensions and add 576 gmolden to dash. Currently the makefile only activates it for the ubuntu 577 linux distro. Probably also works on debian, havent tested that though. 578 579- added the option clean and install to the makefile: 580 581 make install 582 583Tue Dec 1 584 585- for protein structures the first HETATM molecule had NO charges applied 586 when selecting Hydrogen icon -> "Optimise Hydrogens" 587 588- added new keywords to run molden with a command file: 589 590 keywrd: WRXYZ=1-12 591 592 0 xyz file 593 1 mol file 594 2 msf file 595 3 tinker xyz file 596 4 '' '' 597 5 pdb file 598 6 chemx format 599 7 msi format 600 8 molden format file 601 9 mol2 file 602 11 ambfor xyz file 603 12 mopac xyz input file 604 605 This command allows to read in any by molden supported formats and 606 write out the specified format in file 'mol.xyz' 607 608 Sample molden command file: 609 610 title line 611 file=any_input_file wrxyz=11 612 613 This will write a ambfor xyz file. As input you could specify a pdb file. 614 The ambfor xyz file, will have hydrogens added, incomplete residues 615 corrected and charges and hydrogens added to ligands and water molecules. 616 617 keyword: WRMOPXYZ 618 619 Write an mopxyz input file. 620 621 keyword: CHARGE=-1 622 623 Specifies a total charge for the molecule to be written in conjuction 624 with the WRXYZ keyword. 625 626 keyword: WRTAUTO=1-12 627 628 0 xyz file 629 1 mol file 630 2 msf file 631 3 tinker xyz file 632 4 '' '' 633 5 pdb file 634 6 chemx format 635 7 msi format 636 8 molden format file 637 9 mol2 file 638 11 ambfor xyz file 639 12 mopac xyz input file 640 641 Generates enol tautomers from keto forms and writes them as tau01.xyz, 642 tauto02.xyz etc. 643 644 QMPSA calculates the polar surface area 645 646Wed Sep 23 647- Robert Gyepes reported a bug that would ignore the fill setting 648 in the space filling (3D) orbitals rendering in the Xwindows mode. 649 Fixed this. 650 651Tue Sep 15 652- fixed a bug when adding hydrogens to HETATM residues from the PDB, 653 using the plush directory. The first atom in the HETATM residue in the 654 plush directory would have its hydrogens omitted. 655 656Sat Sep 12 657- fixed a bug that would not let you add characters to a string after 658 you did a backspace on the start of a string 659 660Fri Sep 4 661- repaired a minor bug that would not label Hetatm molecules correctly 662 when no water was present in the pdb file. 663 664Wed Sep 2 665 666- Now when a water box is added, water and added ions can be displayed 667 independendly from the "HetAtm" button. 668- Names of HETATM molecules from pdb files are passed on to ambfor .xyz and 669 .arc files and are displayed at such after ready these .xyz files into 670 molden 671 672Thu Aug 20 673 674- Restored proper visualisation of water in the water box added. 675- When creating a crystal from scratch., by first creating a molecule 676 with the z-matrix editor and the chosing "pack cell" from the "cell" 677 icon, chosing "edit cell parameters" (choose P-1). The second molecule 678 related by the inversion symmetry was not shown. Now it is. 679 680Tue Jul 21 681 682- when reading in a pdb file, followed by optimise hydrogen positions, 683 then starting a force field optimisation with water box, connections 684 of water would be wrong. Fixed! 685 686Fri Jul 3 687 688- removed a bug that corrupted shadows 689- the thousends of water on an amb(for/md) xyz file, are now represented 690 as just one HOH in the HETATM drop down list. 691 692Thu Jul 2 693 694- removed an other bug from pdb file writing routine for non-pdb structures. 695 This bug would cause a non-pdb structure to write a pdb file with only 696 a HEADER line. 697 698- When having added a water box and subsequent optimisation with ambfor, 699 the resulting _opt.xyz would crash ambfor when using it to do further 700 optimisations. 701 702- When viewing a ambfor xyz file with a water box added, selecting "backbone" 703 the box would disappear and oddly only reappear when switching on the first 704 HETATM residue. Fixed. 705 Also the color of the box would change to the selected color for the first 706 HETATM residue. 707 708 709Tue Jun 30 710 711- When writing PDB files with labels from the original PDB file 712 this would lead to wrong element labels after z-matrix editing of the 713 structure. Now the PDB file writing routine no longer uses these labels 714 after the z-matrix editor was used. 715 716- The newly introduced labels on a residue basis would run out of its array 717 bounds, especially when many waters were present, causing a segment 718 violation. Fixed. 719 720Molden5.4 721 722- beginning of June 2015: EBI changed their MSD web interface for 723 there PDBE interface. As a result, the CML files of HETATM molcules 724 in the PDB were no longer available. 725 I therefor decided to create a local repository for Molden to get 726 information on hydrogens to add on HETATM molecules. 727 Now a 'plush' directory containing this information is added. 728 729- Added the possibility to clip surfaces. This is especialy interesting 730 for molecular surface of proteins. 731 After creating a molecular surface, you click the "palette icon' -> 732 surface -> clip 733 734Molden5.3 735 736Sat May 30 737 738- After Copying a hetatm molecule to a separate structure: 739 and then saving as pdb file, produced a file containing only 740 the HEADER line: fixed 741 742- The 'plotplane' keywords in the opengl version of molden (gmolden) 743 did not update the screen, giving the wrong impression that nothing had 744 happened. Now the screen does update after plotplane commands such as 745 PHASE. 746 747- In pdb entry 1fj3, Zn has a spurious connection to a H2o, of which 748 only half bond (the zn part) is displayed, the O side is not visible 749 on "contact" of Zn. This is fixed, now also this water is displayed. 750 751Fri May 22 752 753- Sometime back I introduced adding an extra hydrogen on tertiary 754 nitrogens, when adding hydrogens to ligands. Now this will only be done 755 if the three connected atoms to nitrogen do not lie in a plane. 756 757- Added the Label On/Off entry to the popup menu for residues and hetatm 758 molecules. This lets labels be switched on/off on a residue basis 759 rather than on the whole molecule. 760 761Thu May 7 762 763 764- Adjusted rotamer generation for the different form of Histidine 765 (HIE,HID and HIP). 766 767May 1 768 769- Added a alternative way to generate rotamers. 770 771 Previously rotamers could only be changed after generating a z-matrix 772 for a protein. This was because rotamers change was accomplised changing 773 certain dihedral angles in the protein z-matrix. 774 The alternative method, aligns the stored rotamers of a particular type 775 of residue to the actual residue in the protein. To be more precise, it 776 aligns the backbone atoms (Calpha, N, COO and Cbeta). 777 The rotamer editing features are now also available without a z-matrix 778 having been built. 779 As a side effect the option to edit residues have been moved down in 780 the small residue popup window. 781 782- Aligning and Combining two protein strcutures, now conserves displayed 783 residues in the backbone mode. 784 785- The option restore incomplete residues now also makes use of the new 786 rotamer generation scheme. 787 788------------------------------------------------------------------------ 789Molden5.2.4 790 791Wed Apr 15 792 793- Changed a minor detail in the source code for surf, that stops it from 794 core dumping wtih the latest versions of Ubuntu. 795 796Fri Mar 20 797 798- added option to make complete the incomplete protein residues. 799 It is available from the 'H' icon -> Optimise H postions. 800 801- Previous, adding atoms to one of the twenty known protein residues 802 in the z-matrix editor these atoms would be flagged "NewRes". 803 However this was coded in such a way that while changing a amino acid 804 for another one this was also done, which is not correct. 805 Secondly the string for water in the hetatm arrays was overwritten. 806 This has been solved. In addition instead of "NewRes" now a string like 807 "gly.mod" is used to denoted the added atoms. 808 809Fri Mar 13 810 811- With combine/Align structures, now a new structure is created, 812 leaving the two original structures alone. 813 814- Increased the speed of the optimsing water subroutine substantially 815 816Wed Mar 5 817 818- When loading PDB files -> zmat editor -> out if zmat editor -> add H's to 819 HETATM molecule -> zmat editor: the residue variable where not updated and 820 actually displayed the wrong variable. Fixed !! 821 822- when animating residue variables in the z-matrix, in backbone mode: 823 only the animating residue was displayed, the rest disappeared (only molden 824 ,gmolden was OK). Fixed !! 825 826- made changes to the makefile where it calls the makefile in the ambfor 827 directory: no longer are the FFLAGS and CFLAGS exported. 828 When they are exported, they can cause ambfor to thow a lot of NaN 829 (Not a Number: the computer words can not hold the unexceptionally 830 large or small values of the varaible). 831 Until this is completely solved, use a gradient norm not smaller than 0.03 832 833Wed Mar 4 834 835- when writing a pdb file from Molden, the orginal labels of the HETATM records 836 would not be written, causing the add Hydrogens to HETATM not to work with 837 the newly written file. 838 839- In the case of a pdb file read into Molden and subsequently opening the 840 z-matrix editor a z-matrix is made for the protein. When after leaving the 841 z-matrix editor hydrogens are added to HETATM molecules (via clicking with 842 the second mouse button on the molecule on screen, and selecting 843 "add hydrogens"), a new z-matrix has to be created including these newly 844 added hydrogens. This fix creates a new z-matrix in such a case. 845 846 847Fri Feb 27 848 849- When doing a charge calculation on a hetatm (PDB) molecule, only 850 -3,-2,-1,0,1,2,3 were offered to pick from. Now the oprion "other" is added. 851 852- In the "molden file select" window an extra button has been added "Search PDB" 853 Clicking it will bring up a window that lets you search the PDB for keywords. 854 For example "quorum sensing", a list of matching pdb codes will be displayed. 855 When a pdb code is clicked a few lines from the description are displayed. 856 When "Load PDB code" is clicked the pdb structure will be downloaded and 857 displayed. 858 859- a few help strings have been added. 860 861- In the z-matrix when you click a field with the second mouse button. 862 A popup window lets select "animate", which would subsequently animate the 863 result of variable being increased/decreased. 864 The new way will open a window in which the variable can be increase or 865 decreased by one frame as well as animated. 866 During that the window is displayed all other windows will become 867 unresponsive, except the main drawing window, in which you will still 868 be able to rotate/translate your molecule. 869 870- When opening the z-matrix editor on a PDB file, adding hydrogens to 871 HETATM molecules would nolonger work after the mutation of a residue. 872 This has been fixed. 873 874Wed Jan 28 875 876- Molden text editing input handling routines have been updated. 877 They now support dynamic editing: each entry field upon activation 878 now shows a cursor to indicate its position. On that position you can now 879 type characters or delete characters. Whereas previously you could only 880 add or delete at the end of the string. 881 882- make molden now works again (no more unsatisfied external reference ogsel).. 883 884- fixed a small bug with the gif snapshot routine. The top line of the 885 gif image was black or had garbage. 886 887Molden5.2.3 888 889Mon Jan 19 890 891- The optimise hydrogen functionality is now split into to separate parts 892 which can be switched on and off in a small window. 893- GLN/ASN flips will now only be done on complete residues 894- Molden now checks before adding hydrogens to residues if the hydrogen 895 positions is not taken by a bonded atom (covalently bound hetatm). 896- NO Hydrogens are added any longer to PO4 groups from the hetatm section 897 of a PDB file. 898- NO Hydrogens are added any longer to COO (carboxyl) groups from the 899 hetatm section of a PDB file. 900 901Molden5.2.2 902 903Fri Nov 28 904 905- When aligning two molecules the center of rotation was akward; fixed it. 906 907- Molden can now also read gaussian input files with cartesian geometry 908 specification 909 910- Molden can now read in z-matrices with only two lines. Use commandline 911 flag -d to get old behaviour. 912 913Molden5.2.1 914 915Mon Nov 3 2014 916 917- From the Molden interface you can now create .avi movies. 918 This functionality depend on a third party package avconv. 919 (on linux: sudo apt-get install libav-tools). 920 Screen snap shots are made with the .bmp format. 921 922- Fixed bug it the saving bmp function. This bug would only show it self 923 if the screen width was bigger than the screen height. 924 925- Mopac2012 aux files are now better supported. 926 In the submit mopac job window, the keyword AUX is added by default. 927 If you use an older version of mopac, you might want to remove this 928 keyword again. (see xwin.c look for 'AUX'). 929 Added method PM7. 930 931Molden5.2 932 933Wed Oct 22 2014 934 935- Molden can now calculate the Electron Localization Function (ELF). 936 937- Molden can now write .WFN style of wavefunction files. 938 It does not work with the use of 5D or 7F functions. 939 940- When using Molden with gamess-us input files that contain cartesian 941 coordinates, Molden now recognises the use of coordinates specified in 942 angstroms. So now the connectivity is correctly displayed in such cases. 943 944- with commandlineflag -J [0,1,2] molden can now write other screen dump 945 formats than gif [0] such as rgb [1] and bmp [2]. Gif is the default. 946 The high definition formats rgb and bmp are specially useful for 947 creating movies, such as with the ffmpeg package: 948 949 ffmpeg -i mol%03d.bmp -target dvd -s 800x800 movie.avi 950 951- rdbas previously standard read 3dgridfile. 952 Now it can read any file by spcifying it after the rdbas 953 command: 954 955 rdbas=anyfile 956 957- Created two new commands to specify the upper and lower limits of the 958 electrostatic potential treated as polar. This is in aid of the 959 calculation of polar surface area. POLUP=value POLLOW=value 960 961 Example of a keyword file mapping an electrostatic potential grid (mapfil) 962 onto on electron density grid (rdbas): 963 964 title 965 FILE=boxazepam_631g.out RDBAS=d0.3dgrid 966 MAPFIL=m0.3dgrid POLLOW=-0.075 POLUP=0.100 SPACE=0.01 967 968- Molden now has rudimentary support for Mopac2012 output. 969 Full support is provided through the auxilliary file (.aux) mopac 970 creates through the use of the keyword AUX. 971 972Molden5.1 973 974Wed Jan 22 2014 975 976- Updated the ambfor and ambmd codes to run optimisations and MD 977 on proteins faster. This hold for the optimisations with cutoff 978 They now use the Damped Shifted Force protocol by Fennell 979 Gezelter. Also creation of a water box has been sped up. 980 981Molden5.0.7 982 983Fri Jan 10 2014 984 985- Paul Fleurat-Lessard did an update of the molden routines reading 986 VASP POSCAR and XDATCAR files. This was necesary to support a newer 987 version of these files. 988 989- added the keyword 'wrmolf' to ne used in the molden command file. 990 'wrmolf' triggers the writing of a molden format file 'mol.molf' 991 992- update the opengl secundary structure renderings (gmolden) of protein 993 being edit in the z-matrix (and in animated variables). This is important 994 for the psi and psi angles. Now the changes in psi and psi angles are 995 immediately applied to the structures on screen. 996 997- molden compiled with gfortran would sometimes crash on an unexpected 998 end of line. Fixed it. 999 1000- molden format files with multiple sets of coordinates would not be displayed 1001 correctly. 1002 1003- When reading ambfor .xyz files, molden would not set the internal 1004 (molden) variable ipdbt() for C-Terminal OXT residues. This would lead 1005 to a faulty .xyz file written by molden, for instance on subsequent use 1006 of the original file to start further ambfor/ambmd calculations. 1007 1008- When doing from molden a MD run in the background (with ambmd), the first 1009 read in .xyz file (by tnkfst in runjob.f) would lose the reordering information 1010 when more memory was allocated. This resulted strange water connectivity. 1011 Fixed it. 1012 1013Molden5.0.6 1014 1015Tue Apr 9 1016 1017- The functionality of adding hydrogens to hetatm residues was broken due to 1018 change in the web service pdbechem. With this version it is again functional. 1019 1020- gmolden: shader bug when using occlusion and Blur caused the screeen 1021 to not be updated correctly on some systems. 1022 1023- gmolden: Added a proper "balls & sticks" mode, next to the already existing 1024 sticks mode (in gmolden incorrectly named as balls & sticks). 1025 1026Molden5.0.5 1027 1028Thu Dec 20 1029 1030- Added to possibility to localize orbitals (boys scheme). 1031 Next to the 'orbitals' button there is now a 'local' button. 1032 1033Molden5.0.4 1034 1035Mon Nov 26 1036 1037- Added a ramachandran plot for proteins. It can be found as last option 1038 under the 'Surface' icon. 1039- Fixed a bug that made the Average CH3 button disappear in the NMR spectrum. 1040 1041Fri Nov 9 1042 1043- Restructured file selection so that it can now be generally used. 1044 Used the file selector in the "Read Grid" button in the density mode 1045 and also on the "Vr" button where you can map an other grid onto the 1046 first grid. 1047 Added a filter to the file selector, nothing fancy just a substring match. 1048 1049- Cleaned to code of molsint.f. Now when calculating distributed multipoles 1050 Molden will report when mxsite is exceded. This usually only happens when 1051 NO overlap contributions are shifted to atomic sites. 1052 1053- Somebody reported problems on his self constructed gaussian style files. 1054 Fixed this. 1055 1056- Added a charges scaling option to ambfor (for example : ambfor -S 0.7) 1057- Ambfor will now parse a file called 'param' with alternative parameters 1058 (If it exists of course). 1059 1060 1061Thu Sep 20 1062 1063- Molden now by default no longer searches for mpi executables at start up. 1064 On machines with terabytes of disks this can take very long. 1065 1066- Updated reading of Orca files, so that geometry+gradient single point runs 1067 should now also be supported. 1068 1069Thu Sep 13 1070 1071- Molden can now also read Gamess-US inputfiles with cartesian coordinates 1072 1073- Adjusted the writing of ambfor .xyz files so that the file can still be 1074 read by molden if there is an undefined atom type. 1075 1076Fri Jul 13 1077 1078- Molden used to read in the first point with orbitals for Gaussian09 1079 This was because in the beginning of its release, the orbitals 1080 of the stationary point were not printed. 1081 Currently Gaussian09 does print the orbitals of the stationary point. 1082 Now Molden will display the orbitals of the stationary point. 1083 1084Fri Jun 15 1085 1086- Molden now check then openGL vendor string to circumvent a bug 1087 in the graphic drivers of intel video cards. 1088 This caused a segment violation on _mesa_generate_mipmap 1089 1090Thu Jun 7 1091 1092- the .jdx file written with the use of the keyword PLECTRUM now 1093 also contains information for use in combination with jspecview 1094 and jmol. 1095 1096Thu Apr 26 1097 1098- included wrting of a .jdx file with the keyword PLECTRUM 1099- keyword SPACE=value now is honoured when reading cube/grid files 1100 1101Thu Mar 15 1102 1103- Made the generated web pages for spectra (keyword PLECTRUM) compatible 1104 with Internet explorer. 1105 1106Tue Feb 28 1107 1108- Improved generation of the html page created with the use of the 1109 PLECTRUM keyword. (see below Tue Feb 14). 1110 The command used to convert the postscript file now is: 1111 1112 gs -sDEVICE=jpeggray -g1000x500 -dBATCH -dNOPAUSE -sOutputFile=spec.jpg spec.ps 1113 1114 The index.html file now also contains javascript code to view the 1115 active normal mode as a red line drawn on the spectrum. 1116 It also contains a table of available frequencies together with intensities, 1117 they can be clicked. 1118 1119Tue Feb 14 1120 1121- The molden keyword PLECTRUM calculates a spectrum for files that have 1122 frequency and intensity information, in addition it converts the 1123 postscript file that contains the spectrum to a jpg file. 1124 For the conversion to work the ghostscript program must be installed 1125 and defined. The folowing command is used to generate spec.jpg: 1126 gs -sDEVICE=jpeg -r500x250 -dBATCH -dNOPAUSE -sOutputFile=spec.jpg spec.ps 1127 It also creates the files index.html, mol.xyz and freq???.xyz. 1128 The last files contain animations of the normal modes. These can be used 1129 for interactive spectra in combination with the jmol viewer. 1130 1131- Rudimentary support for NWchem output files. 1132 1133Mon Feb 13 1134 1135- The xyz format already supported dummys with the 'xx' element label. 1136 Now Banquo ('Bq') sites are also supported. Both are displayed with the 'xx' 1137 label. 1138 1139Fri Feb 02 1140 1141- Added molden keywords SPECTRUM (and PLECTRUM) to calculate a spec.ps 1142 from a molden commandfile. Only for files that have spectra information. 1143- Molden now visualizes a file with just one atom better. 1144 1145Fri Jan 20 1146 1147- Added keywords EXTPOSCHG and EXTNEGCHG which specify a single pointcharge 1148 to be added for the calculating of the QM electrostatic potential. 1149 This can be used to model a counter charge when calculating the Elec. 1150 Pot. of an anion or cation. 1151 EXTPOSCHG=(r.rr,r.rr,r.rr) where r.rr is a real number representing 1152 the cartesian coordinates in Bohr. 1153 1154- Added commandline flag -U to switch of using shaders. On some graphics 1155 cards the opengl version (gmolden) can hang on setting up the shaders. 1156 1157Mon Jan 9 1158 1159- Some optimisation to shader code for the benefit of older graphics 1160 cards under Ubuntu Natty 1161 1162Sat Dec 31 1163 1164- The lines representation of a surface in Opengl shader language 1165 gave problems. Fixed it. 1166 1167Thu Dec 1 1168 1169- Molden uses the pdbechem service to find out what hydrogens to add 1170 on ligands. Unfortunately, the URL for this service has changed. 1171 I have updated Molden to point to the new URL. 1172 1173Mon Nov 28 1174 1175- Fixed blocky noise when using occlusion. 1176 1177Mon Oct 24 1178 1179- amfor xyz files with cell information were not correctly stored in 1180 the internal common blocks of molden. 1181 As a result writing a just optimised structure and comparing it with the 1182 structure on screen would give different results. 1183 Fixed it ! 1184 1185Sun Oct 23 1186 1187- Reading molden format files that contain only data for MO coefficients 1188 that are non-zero. When this file is not the first file read in 1189 it could occur that coefficinet that should be zero were actually non-zero. 1190 Fixed this. 1191 1192Fri Oct 21 1193 1194- Fixed small bug that would leave a atom selected in solid mode hovering 1195 around when switched to line or stick mode. 1196- gmolden using shaders would sometimes not draw a surface as transparent 1197 1198Mon Oct 17 1199 1200- Added a bigger font for the labels of atoms and residues for the opengl 1201 version gmolden. 1202 1203Wed Oct 12 1204 1205- added the commandline option '-k int' (int=0-15), to specify the 1206 color used to plot lables. Only available for the openGL version (gmolden). 1207 1208Thu Sep 29 1209 1210- The by molden created *.ogl files can now also be read from the commandline: 1211 ./gmolden molden.ogl 1212 Previously, these files could only be read from the filemanager. 1213 1214Wed Sep 28 1215 1216- fixed a bug that would leave the outvector of the plotplane essentially 1217 as a nul vector. This would only occur if you let molden figure out 1218 a default plane AND if the first three atoms would be on a line. 1219 1220Fri Sep 23 1221 1222- Built in a button to make a gif screen shot in the density mode. 1223- Pressing 'R' for shadows now does not make the background black when 1224 no shader capability is found. 1225- when writing a ambfor .xyz file with crystal information, now also 1226 expands the cell before writing. 1227 1228Thu Sep 15 1229 1230- GAFF atom type assignement: switched from default aromatic Nitrogen 1231 type nb to nc. (nb is only for pure aromatic compounds such as pyridine) 1232- also truncated negative values (see Wed Sep 14). 1233 1234Wed Sep 14 1235 1236- fixed problem with writing cube files on 64-bits platforms. 1237 Function values that are less than 1.0d-99, are 'truncated' to 1238 1.0d-99 1239 1240Mon Sep 5 1241 1242- Fixed a bug in the C code that calls getpoi (Thanks to Ben Roberts, 1243 University of Florida for fixing this). This bug could affect the 1244 processing of Gaussian files. 1245 1246- When there is only one (hetatm) molecule in a PDB file, molden would 1247 not pass on the total charge to the routines that calculate partial charges, 1248 even when it offered the possibility to set it. Fixed. 1249 1250Thu Sep 1 1251 1252- when the main window was resized (or -geom commandline option was used) 1253 in the opengl version (gmolden), the rubber selection band for selecting 1254 atoms in the z-matrix editor was wrongly displayed. This is now fixed. 1255 1256- when assingning charges to hetatm molecules of pdb files, molden would 1257 try to retrive the total the total charge from the pdbchem. If no valid 1258 three letter residue identifier was defined it would return charge option 1259 -15, as a result the default total charge in the "assign total charge" 1260 window would be "quintet" in stead of "0". Such a situation would accur 1261 when a ligand was added by combination of two structures in the structures 1262 window. 1263 1264Thu Aug 18 1265 1266- When using xming as xwindows/opengl emulator, in the opengl mode when 1267 using the "select by pointer" mode in the z-matrix editor, the rubberband 1268 would not be drawn. This is now fixed. 1269 1270Tue Aug 16 1271 1272- When writing a Gamess-US style z-matrix and when variables were specified 1273 as constants, Molden now writes an ifreez record and nzvar. 1274 1275Wed Aug 10 1276 1277- Added visualisation of calculated UV-spectra from TD-DFT calculations with 1278 Gaussian. Please feel free to suggest improvements. 1279 1280Mon Aug 8 1281 1282- Fixed a bug which could make molden crash when having multiple structures. 1283- The output of the internally run 'locate' command on linux is now redirected 1284 to /dev/null. So unsuspecting users are not confused. 1285- Added small tweaks to the gaff forcefield types assignment (nitrogen in 1286 cyanide is now typed). 1287- Added a lot of ifdef statements to make sure older linux distributions 1288 do not include the newer code for OpenGL shaders. 1289 1290Mon Aug 1 1291 1292- Fix for reading gaussian 09 output when coordinates were frozen. 1293 1294Wed Jul 13 1295 1296- reading of esp charges on gaussian output has now been put before reading of 1297 basis-set. This way when no basis-set is written the esp charges 1298 will still be read. 1299 1300Mon Jul 4 1301 1302- The 3D wireframe drawing (X-windows) of the density/orbital mesh was 1303 no longer drawn with equal width and height when using the commandline 1304 -geom 1600x800 qualifier (example). Fixed it. 1305 The use of shadowmaps currently only works if you dont resize. 1306 1307Thu Jun 30 1308 1309- Introducing Shadow mapping, for proteins, the secondary structure cartoons 1310 cast shadows on them selves. See the palette icon, option shadows. 1311 Or just hit 'r' in the drawing screen. 1312 1313Tue Jun 7 1314 1315- Introduced a bug in reading multi xyz formats, some month ago. Fixed it. 1316 1317Tue May 31 1318 1319- There was a bug reading Mopac2009 output 1320 1321Mon May 16 1322 1323- Molden now prevents the jobname being the same as the file being currently 1324 read. This can cause problems. 1325 1326Wed May 12,13 1327 1328- Removed a bugs from the mpi MD code. 1329 1330Thu May 5 1331 1332- gmolden will draw proteins faster in the space filling mode. 1333 1334Wed May 4 1335 1336- gmolden would be killed due to too much memory consumption, during an MD 1337 run, fixed. 1338- xyz files containing more than 1000 structures, are now all accounted 1339 for in the geom conv. window. 1340 1341Thu Apr 28 1342 1343- There is a bug detected in the fast water code of ambmd. I have 1344 applied a temporary quick fix. 1345 1346Tue Apr 12 1347 1348- Added postprocessing options: Blur and Occlusion to the colorpalette 1349 icon. These options work as toggles. It will slow this down a bit, 1350 certainly on less powerfull systems (graphics card dependant). 1351 This is only available if you run molden locally. 1352 1353- Changed the default for gmolden (mixed openGL/Xwindows executable) 1354 to be fullgl. You can still get the old mixed behaviour by using the 1355 commandline option -F. 1356 1357- Molden does now also better support the mol2 file dialect used by 1358 the popular docking program FlexX. 1359 1360- When calculating the contacts between a ligand and residues in opengl 1361 mode, the distance labels where not correctly displayed at far away 1362 distances. Fixed it. 1363 1364Wed Apr 6 1365 1366- input z-matrices having variable names longer than 8 characters were 1367 not read in. I have now increased the maximum variable lenght to 10. 1368 1369Wed Mar 16 1370 1371- Molden now has per pixel lighting built in. This looks a lot better, 1372 especially the specular lighting. The per pixel lighting is accomplished 1373 with shaders. Windows emulators like Xming and Xwin32 do not support shaders, 1374 so you will not see a difference there. 1375 1376Mon Mar 14 1377 1378- Molden compiled with gfortran had problems with reading the protein 1379 density file, fixed it. 1380- Molden compiled with gfortran sometimes crashed when reading in a 1381 second structure, fixed it. 1382 1383Wed Mar 2 1384 1385- Added a cutoff scheme for water-water interaction, see: 1386 1387 Is the Ewald summation still necessary? Pairwise alternatives to 1388 the accepted standard for long-range electrostatics 1389 Cristopher J. Fennell and J. Daniel Gezelter, 1390 Journal of Chemical Physics. 124, 234104 (2006) 1391 1392- Adapted the makefile to be a little more intelligent. 1393 It now tries to figure out on what os it is. This will cover most 1394 flavors of linux, MacOSX and cygwin. 1395 1396Fri Feb 25 1397 1398- Added support for the Gaussian 09, new IRC mode HPC. 1399 By request of Prof. Ugo Cosentino 1400 1401Thu Feb 17 1402 1403- added a routine for water-water interections. It uses a lookup table. 1404 It is unfortunately only a little bit faster (factor 0.66) 1405 1406Fri Feb 11 1407 1408- removed a bug that would not copy all of the force field information 1409 after allocating memory for a water filled box. 1410 1411Thu Feb 3 1412 1413- Adding ions is now done depending on the electrostatic potential. 1414 You can still invoke random placement with the commandline argument 1415 -z on ambfor/ambmd (in combination with -b). 1416 1417Wed Feb 2 1418 1419- replaced use of fork by vfork in an attempt to stop forking errors 1420 on windows7 (64bits version still has problems). 1421- When adding a water box in ambfor or ambmd automatically ions are 1422 added to neutralise the box. The placement of the ions is accomplished 1423 by replacing waters randomly 1424 1425Fri Jan 28 1426 1427- there is now also a multiprocessor version of the crystal optimiser. 1428- removed a small bug in the opengl version when reading a jaguar cube 1429 file. 1430 1431Tue Jan 25 1432 1433- The molden/gmolden interface will now automatically detect whether the 1434 openmpi executables have been built. If so an option to use multiple 1435 processors will be availabe in the window that fires ambfor/ambmd jobs. 1436 1437- Removed a bug in the multiprocessor version of the MD program, ambmd. 1438 Each subprocess would have its own initial velocities, which in turn 1439 would lead to different coordinates in each subprocess. Fixed it. 1440 1441Thu Jan 13 1442 1443- Finally got the interactive optimisation working flawless on 1444 WindowsXP. 1445- Fixed continued rotation during interactive optimise. 1446- optimised update time during optimisations 1447 1448Wed Jan 5 1449 1450 - Added atom type 'cz' to the GAFF force field, this is needed for guadinium 1451 and arginine. Also added improper torsion to keep the C connected to the 1452 three N's in one plane. 1453 1454Tue Dec 7 1455 1456- Crystal optimiser was only working for non-covalently bound crystals. 1457 Current version has been tested on organic crystals and seems to work. 1458 1459Molden5 1460 1461- Added a crystal optimizer, based on the gaff force field. 1462 Periodic conditions are enforced by translation symmetry copies. 1463 NO ewald summations ! This is a beta test. 1464 1465- Gamess-US irc data, bug fix. first atom was not displayed 1466 1467- While adding support for the calculated NMR spectra, a bug was introduced 1468 that made it impossible to set the maximum intensity in a spectrum. 1469 fixed. 1470 1471- When doing a combine structure on two proteins, the ligands are now also 1472 colored by structure. 1473 1474- When using combine + align on two none protein structures, the user 1475 is asked to specify 3 pairs of atoms. Each pair consisting of one 1476 atom from the first and one atom of the second molecule. The code 1477 has been changed in such a way that only atoms can be selected 1478 of the first/second structure. 1479 1480- Adapted molden to be more vista/windows7 friendly. 1481 1482- When aligning two structures no longer the pmf score window pops-up 1483 after pressing escape two or more times. 1484 1485- the interface to qchem and orca was only partly functional. Fixed it. 1486 1487- The crystal information of a mol2 file was nolonger parsed, fixed it. 1488 1489------------------------------------------------------------------------ 1490 1491Molden4.9 1492 1493Wed Sep 22 1494 1495- Updated molden to read gaussian09 IRC caclulations outputs. 1496 1497Wed Aug 11 1498 1499- Updated Updated reading of Gamess-us output, kindly supplied by 1500 Mariusz Klobukowski. The number of electrons when using pseudopotentials 1501 is also calculated correctly. 1502 1503Mon Jun 21 1504 1505- Updated reading of Gamess-us output, kindly supplied by Mariusz Klobukowski 1506 1507 1) to read results from hessian calculation in the latest version of 1508 gamess-us (lines with mode symmetry information were added) 1509 1510 2) to read basis sets in semiempirical calculations (we changed gamess-us 1511 to be able to see the semiempirical MOs, with the STO basis sets expanded 1512 in terms of STO-nG expansions). 1513 1514Thu Jun 17 1515 1516- The reading of a gridkont file (Program GRID) has been moved from the 1517 density mode to the molecular mode. Under the surface icon, there now is 1518 an option "gridkont". The benefit of this move is visualisation of the 1519 GRID molecular interaction together with the full opengl protein 1520 visualisation and the use of clipping planes. 1521- added a box around the grid for gridkont and protein electron density. 1522 1523Wed Jun 2 1524 1525- Added the option to for the electron density to follow the current residue. 1526 This build on a feature of molden to show the label of the residue 1527 the pointer is currently over. In addition now also a block of 1528 electron density follows the residue the pointer is currently over. 1529 You can fix the postion of the block, by hitting the spacebar. 1530 Hitting it again will make the block follow the pointer movement again. 1531 This all in the context of the latest hanges to molden of Fri May 28. 1532 See below. 1533 1534Fri May 28 1535 1536- Under the surface icon, there was the option electron density map. 1537 Clicking this would try to read a file contaning protein electron 1538 in the so called 'omap' or DSN6 format. These files are available 1539 from the Electron Density Server at Uppsala University: 1540 1541 http://eds.bmc.uu.se/eds/ 1542 1543 This functionality has been extended. When reading a pdb file the pdbid 1544 is automatically parsed and stored. When clicking the "elec. Dens. Map' 1545 option the pdbid is used to automatically retrieve the omap file from 1546 the electron density server. (the program wget is used for this). 1547 1548 After the file is read, a window will pop up, where you can specify the 1549 electron density contour level. The rendered electron density volume 1550 can also be clipped in three directions, for clarity. 1551 1552- on request from Paolo Tosco, molden4.9 now allows upto four keyword lines 1553 in a molden keyword file. 1554 1555Wed Apr 21 1556 1557- When reading a protein ambfor .arc file, the secundury structure would be 1558 all coils, fixed this. 1559 1560Mon Apr 19 1561 1562- When interactively omptimising a structure with a water box, molden 1563 sometimes would not show the waters. Also aborting the optimisation 1564 by pressing escape, would sometimes disrupt the X protocol. 1565 Fixed. 1566- Updated the windows version. 1567 1568Wed Apr 14 1569 1570- When a ambfor xyz file was loaded after a pdb file, its secundary 1571 would be all coils. Fixed. 1572 1573Tue Apr 13 1574 1575- When reading a ambfor xyz file, nolonger the hydrogen bonds are 1576 calculated by default. In the presence of a big water box this becomes 1577 very slow. 1578 1579- Going into the zmatrix editor the waters were stored. After quitting 1580 the zmatrix editor, the waters were restored. However in the presence 1581 of a large water box, the restoration was very slow. Fixed. 1582 1583- Using the default optimiser(lbfgs) now also the waters that water out 1584 of the box are come in to the other side of the box. 1585 1586Mon Apr 12 1587 1588- When interactively optimising a small molecule , in the presence of 1589 water box, the waters and box would not be visible in the line drawing 1590 mode (solid was ok). Fixed. 1591 The box itself is now also visible. 1592 1593- In the residue command window, when multiple chains were available, 1594 you would have to specify the chain also in order to visualise residues. 1595 This is now changed. You can however still use the chain identifier: 1596 *:A for example will switch on all residues belonging to the A chain. 1597 1598- When reading an ambfor xyz file containing a protein, and subsequently 1599 writing a PDB file, every first residue of a chain had residue number 1. 1600 This caused probelms when there were chains consisting of 1 residue. 1601 Such a pdb file would not parsew correctly. Now all residues have a unique 1602 number. 1603 1604- reading an ambfor xyz file with a box specified, would lead to an empty 1605 screen when opening the z-matrix editor. This is fixed. 1606 1607- When optimising the Hydrogen positions, waters that are close to a metal 1608 center now also have hydrogens added. 1609 1610- Water boxes containing more than 5000 waters would have a corrupt [RESIDUE] 1611 section in the ambfor xyz file. This would lead to artifact in visiulisation 1612 with molden. 1613 1614Wed Apr 7 1615 1616- ambfor: made ff99sb the default protein force field. The unmodified 1617 amber 99 force field will be used when specifying the -x 1618 commandline flag 1619 1620- ambfor: for rna/dna modelling the ff99bsc0 modification of the amber 1621 force field will be used when specifying the -y 1622 commandline flag 1623 1624- fixed a bug that would visually screw up the secundary structure, when 1625 in the xwindow mode. 1626 1627- in the standard molden xwindow version the residue popup windows, 1628 would have options, when clicked would activate the wrong action. 1629 This bug was introduced the week before. 1630 1631Thu Apr 1 1632 1633- absolute scores for histidines were still to big, relative scores 1634 were already OK. 1635 1636- fixed a bug is the secundary visualisation, which under very special 1637 circumstances would not show part of the coil. 1638 1639- The small amino acid menues you can bring up by clicking with the second 1640 mouse button now also contain an option to change the protonation states 1641 for histidine, and a flip option for asn and gln 1642 1643- In ambfor the total charge on non amino acid residues is checked and 1644 corrected if it does not add up to a discrete integer. 1645 1646 1647Thu Mar 25 1648 1649- fixed a major bug in calculating the scores for histidine (D,E,+), 1650 under the optimise hydrogen positions. 1651 1652- added prediction of asn/gln flips, under the optimise hydrogen positions 1653 1654Fri Mar 19 1655 1656- Fixed a bug that could make the hetatm residues disappear in the z-matrix 1657 editor, when previously "Opt H pos." was used. 1658 1659- when aligning two protein structures, both structures have a different color. 1660 Also in the backbone mode the secondary structure visualisation will have a 1661 different color per structure. 1662 1663- when combining two small molecules from the structure window, you will now 1664 be asked to move the two structures into visible range. 1665 1666- when using command from the residue command window in combination with 1667 the SURF keyword, molden will now display opengl surfaces in opengl mode. 1668 1669- cysteines missing an HG atom will now have partial charges adding up to -1. 1670 This also implemented in ambfor. 1671 1672- some pdb structures containing hydrogens with labels not recognised by 1673 molden are now recognized. There are probably more, let me know 1674 if you find more. 1675 1676- fixed a bug that would make some surfaces not being displayed in the 1677 surfaces window. This could also cause: surface OFF, not to work. 1678 1679Mon Mar 8 1680 1681- added ambfor support for modified nucleotides such as: 1682 1683 1MA,5MC,OMC,2MG,M2G,7MG,OMG,YG,H2U,5MU,PSU 1684 1685 NOT supported are: 1686 1687 1MG,I,+U 1688 1689- water oxygen atoms connected to the protein are disconnected before 1690 writing ambfor xyz files. 1691 1692 1693Wed Feb 24 1694 1695- fixed a minor bug that would give a superposed atoms in z-matrix, 1696 after doing optimise hydrogen positions on a dna molecule. 1697 1698Tue Feb 23 1699 1700- for rna to z-matrix molden now takes an OXT atom in to account. 1701 1702Mon Feb 22 1703 1704- Added parameters for nucleotides to the amber force field implementation 1705 in molden and ambfor. 1706 1707- corrected charges for water, which did not completely add up to zero. 1708 1709Mon Feb 1 1710 1711- G09 has different zmatrix output than G03. Molden can now deal with this. 1712 1713Tue Jan 26 1714 1715- Molden4.9 introduces to optimisation method lbfgs as default optimisation 1716 algorithem for Ambfor. Together with some other code optimisations, this 1717 increases the speed of ambfor with a factor 4. 1718- changed param.f, such that less continuation lines are used. 1719 The many continuation lines caused problems with compilers such as ifort. 1720 1721Wed Dec 23 1722- more bug fixes concerning interaction between Molden with Tinker and Ambfor. 1723 1724Tue Dec 22 1725 1726- MAJOR Bug fixes concerning interaction between Molden with Tinker and Ambfor. 1727 For ambfor the bug was introduced on 27 November, when the writing of ambfor 1728 xyz files was changed. This bug is now fixed. 1729 1730 Ambfor will now write a file 'ambfor.wr' to indicate it is writing 1731 intermediate optimisation files, when done writing it will remove this 1732 lock file. This improves the interaction with Molden, which in some cases 1733 would begin to read the file when its writing was not yet complete, resulting 1734 in incomplete structure on screen. 1735 1736 The interface with Tinker was compromised earlier when ambfor started to 1737 write intermediate files in binary form. Tinker and Ambfor now have their 1738 own reading routines. 1739 The jobname.run file, a csh script now has a -f added to the #!/bin/csh 1740 line. This is because .cshrc files could contain commands preventing the 1741 succesful executing of this file. 1742 An number of buttons not applicable to Tinker jobs are now nolonger visible 1743 in the Tinker optimise window. 1744 1745Sat Dec 19 1746 1747- fixed a small bug that interfered with wget, which molden uses to 1748 fetch pdb and hydrogen positions to add to ligands. 1749 1750- fixed a bug that would make ambfor crash when using the -N option 1751 in combination with a liagnd being present 1752 1753Thu Dec 17 1754 1755- The switching function for the electrostatic used with cutoff with ambfor 1756 caused distortions of the final protein geometry. I switched to a 1757 shifting function for the electrostatics to solve this problem. 1758 1759- The use of switching/cutoffs (commandline flag -N) in ambfor/ambmd 1760 is now twice as fast. 1761 1762Mon Dec 14 1763 1764- Open shell stuctures are now also read from a Mopac2007 .aux file. 1765- Molden now tries to find the environment variable g09root 1766- Fixed a small bug that could make Molden crash after reading in two 1767 large structures. 1768- Fix that treats negative J-couplings correctly (NMR from gaussian) 1769 1770Thu Dec 10 1771 1772- In addition to 1H NMR, molden now also calculates the 13C NMR spectrum. 1773- The magnetic shielding and J-coupling corresponding with rotationally 1774 equivalent Hydrogens can be averaged by clicking the corresponding 1775 Button. 1776 1777Wed Dec 9 1778 1779- Molden can now display caculated H NMR spectra from gaussian 1780 You need to have caculated magnetic shieldings and J-couplings 1781 1782Mon Nov 30 1783 1784- Fixed bug in reading nmr data from gaussian output. 1785 1786Fri Nov 27 1787 1788- Ambfor can now be run using cutoff's and switching functions: use the -N 1789 commandline flag to use cutoffs and switching. This can be faster than 1790 all atom optimisation ( a lot). 1791 The window form which ambfor optimisations can be fired from Molden 1792 now also has a button to use cutoff's and switching. 1793 1794- When writing ambfor files the order is now such that ambfor can 1795 work with contigous molecules. The ambfor file now contains an extra 1796 sections '[RESIDUES]' which contains the begin of amino acids and 1797 hetatm ligands (including water). 1798 1799- The ambfor and ambmd now catch the user's Control-C and now flush the buffer 1800 before exiting. 1801 1802- Ambfor now handles better finding equivalent parameters for covalently linked 1803 ligands to aminos acids. 1804 1805- Ambfor can now be run using cutoff's and switching functions: use the -N 1806 commandline flag to use cutoffs and switching. This can be faster than 1807 all atom optimisation ( a lot). 1808 1809 1810Fri Nov 20 1811 1812- When using Gaussian with the keyword NMR, the nuclear shieldings 1813 are read and can now be displayed as a label. If also J-couplings are 1814 available and extra "J" button will appear in the "calculate" section. 1815 When clicking it, select two atoms and the their J-coupling is displayed 1816 in the calculate window. 1817 1818Sun Nov 15 1819 1820- Removed a bug that affected the prediction of HID/HIE histidine 1821 residues. 1822 1823Tue Nov 10 1824 1825- Optimisation of Hydrogen positions under "H" icon, now also includes 1826 getting the formal charges of HETATM residues, adds hydrogens if not added 1827 already and calculates the partial charges of the hetatm residue. 1828 It then optimises the OH positions of THR, TYR, SER resiudes. 1829 Then it optimises the the choic between HIE and HID histidine residues. 1830 Finally it adds hydrogens to the water molecules , that are in close contact 1831 with the protein. 1832 1833- the atom attributes window now also offers an editable field for the atom 1834 number. Which makes it easier to identify an atom on screen, when only 1835 its atomnumber is known. 1836 1837Wed Nov 4 1838 1839- The generation of charges on a pdb file is now more verbose. It also 1840 does nolonger consider the amino acids, since they have charges from 1841 the ambfor forcefield. For each HETATM residue, the charges are 1842 calculated separately. 1843 1844- Molden now also writes HETATM residue names, when writing a PDB file 1845 via the "write" button. 1846 1847- When charges are calculated for a HETATM residue, the VDW surface 1848 colored by electrostatic potential is now supported. 1849 1850Tue Nov 3 1851 1852- The Hydrogens added to HETATM residues, are now put directly after 1853 the the residue. This way it does not interfere with other fucntionality 1854 such as interactive docking and interactive optimalisation. 1855 1856Sun Nov 1 1857 1858- Removed bug parsing PDB entries like 1eat, which have more than 1859 two alternative residues 1860- Made routines to add hydrogens to HETATM residues crash proove 1861 when no residue is recognized. 1862 1863Thu Oct 29 1864 1865- added routines to add hydrogens to HETATM residues from the PDB. 1866 1867 The default uses the web server from PDBeChem. 1868 It uses the external program 'wget' for this. 1869 If you dont have it, you can retrieve it from: 1870 http://ftp.gnu.org/gnu/wget/ 1871 1872 A second fallback method adds hydrogens by looking at the angles of the 1873 atom it coonects to. This method is far from ideal or unambiguous 1874 1875- added the possibility to retrieve a PDB file from the internet. It uses the 1876 external program 'wget' to do this (see above). 1877 You will find a "Get PDB" button and text entry field in the file selector. 1878 1879- When element information is available from columns 77,78 in the HETATM 1880 record of the PDB file, this is now used to determine the element type. 1881 The old method, which uses the atom label to determine the element type, 1882 is still used for old style pdb files. 1883 1884 1885Wed Oct 21 1886 1887- Sometime back the MS-DOS fileformat check was introduced, for files 1888 supplied at the commandline (for files via the file select window 1889 this was already in place). 1890 However, when a non-existent file was specified, an empty file with 1891 that name was mistakenly created. This is now fixed. 1892 1893- In case that there are intensities together with frequencies, both are 1894 now listed together in the frequency list box. 1895 1896Tue Oct 20 1897 1898- when reading a pdb structure from the commandline, followed by 1899 2nd mouse button click on and hetatm residue -> "Mol. -> Structure" 1900 molden would crash. Fixed it. 1901 1902Mon Oct 19 1903 1904- Added optimisation of water to the H optimise option. 1905 Waters acting as donors/acceptors to a residue, have hydrogens added. 1906 Other waters are deleted. 1907 1908- An error in reading AMBFOR .xyz files no longer leads to an exit from 1909 the program. 1910 1911- when reading an AMBFOR .xyz file, the error printing has now improved. 1912 1913- removed a bug in ambfor (which can reveal it self after new memory 1914 allocation. 1915 1916Mon Oct 12 1917 1918- Changed the default for a histidine residue to be Neutral (HID). 1919 The option under the H icon, "Opt. Ser/Thr/Tyr/His H", will now 1920 also select which histidine is the best HID or HIE (both neutral). 1921 positive HIS has to be created via the z-matrix by adding a H to 1922 the neutral histidine. 1923 1924- In Opengl mode structures would not be updated after zmatrix editing 1925 of a protein, fixed. 1926 1927Fri Oct 9 1928 1929- removed bug that would switch hetatms to visible when in backbone mode, 1930 after setting a distance monitor. 1931 1932- when switching from stick to solid in gmolden (opengl) already set 1933 distance monitors would no longer be visible. Fixed it. 1934 1935- Fixed a bug that sometimes would ambfor crash when allocating more 1936 memory 1937 1938- added the option the optimise the hydroxyl hydrogens positions of the 1939 threonine, serine and tyrosine residues. Under the H icon. 1940 1941Mon Oct 5 1942 1943- removed bug which under certain conditions would not correctly show 1944 the opengl secondary structure of the second structure read in (gmolden). 1945 1946Fri Oct 2 1947 1948- Some more fullgl opengl version of gmolden updates. 1949- removed opengl helices/strands/coils during an optimisation, since 1950 they were not updated. 1951 1952Thu Oct 1 1953 1954- The fullgl opengl version of gmolden (as opposed to the mixed xwindows/opengl 1955 version) has a few bugs fixed. In the lines mode, during an protein movie 1956 the residues would not be updated. Now they are. 1957 1958- The distance monitor now also works during a protein movie. 1959 1960Mon Sep 28 1961 1962- when creating a water filled box with ambfor/ambmd, some of the waters 1963 at the edges could be very close to waters in neighbouring cells. 1964 When using this box in MD this would result is waters with very high 1965 velocities. This problem is fixed now. 1966 1967Thu Sep 24 1968 1969- Gaussian09 MP2 energies are now correctly read. 1970 1971Fri Sep 18 1972 1973- Fixed a problem introduced in molden4.8 with reading AMBFOR xyz files. 1974 specifically recognising protein structure. 1975- fixed some of the things that dont work when running the full opengl 1976 version of gmolden (-F commandline) flag. There still remain 1977 some issues. 1978- The zmatrix is NO LONGER updated during a movie 1979- Scroll wheel now also work in interactive optimisation mode 1980 1981Thu Sep 17 1982 1983- more updates to swooth the interaction between molden/gmolden and 1984 ambfor/ambmd 1985- You can now add a water box to both force field and md simulation. 1986- When ambfor xyz/arc files are read in, the element types are mapped 1987 from the integer atom type, and nolonger from the atom label 1988 1989Fri Sep 11 1990 1991Molden4.8 1992 1993- Molden4.8 introduces ambmd: 1994 Added a simple isotropic MD program to the ambfor program. 1995 The Molden interface can now fire these MD jobs via the optimise (AMBFOR) 1996 window. You can now select 'ambmd' in addition to ambfor. 1997 1998- the ambfor and ambmd programs now have a -b commandline flag, which 1999 will add a waterbox to your structure 2000 2001- ambmd produces a .arc file as the trajectory file. The reading of 2002 this file in molden has been speeded up. 2003 2004Wed Sep 2 2005 2006- When adding the possibility of contraints to optimisation with 2007 ambfor, it was overlooked that in the event that no restraints 2008 were set, all atoms in the ambfor xyz file would be treated as fixed. 2009 This has now been corrected. 2010 2011- Water was not handled well in ambfor, fixed it. 2012 2013Thu Aug 27 2014 2015- Added a simple isotropic MD program to the ambfor program. 2016 The Molden interface can now fire these MD jobs via the optimise (AMBFOR) 2017 window. You can now select 'ambmd' in addition to ambfor. 2018 2019Thu Aug 20 2020 2021- When reading G09 output, molden now correctly deals with the fact 2022 that G09 only prints orbitals for the input geometry and nolonger 2023 prints orbitals of the stationary point. 2024 2025- Molden now also recognizes MSDOS files supplied via the commandline 2026 and automatically converts them to unix formatted files. 2027 2028Wed Aug 12 2029 2030- reading back in ambfor generated xyz files, the amber atom types 2031 have automatically charges assigned 2032 2033Tue Aug 11 2034 2035- further compatability fix for reading g09. 2036 2037Thu Jul 23 2038 2039- fixed serious bug in reading gaussian output, while creating support 2040 for g09. Fixed ! 2041 2042- reading back in ambfor generated xyz files, the supported amber ions 2043 are now correctly classified by element. 2044 2045Tue Jul 21 2046 2047- first support for gaussian 09 2048 single point, simple optimise, simple force/freq jobs supported 2049 More updates are probable to follow 2050 2051Sun Jul 19 2052 2053- Removed a number of bugs concerning reading the latest Gamess-UK 2054 output. 2055 2056Fri Jul 17 2057 2058- Reading gamess-uk output with more than 99 points in the 2059 geometry optimisation, all point above 99 would not be updated, fixed it. 2060 2061- The energies from the latest Gamess-UK output are picked by molden 2062 and shown in the geom. conv. window. 2063 2064- The fullgl version of molden would not update the background color when 2065 changed with the paleete icon: fixed 2066 2067 2068Wed Jul 15 2069 2070- fixed recently introduced bug, reading 3dgridfile 2071 2072Mon Jul 13 2073 2074- Partial optimisation can now run in BFGS optimisation mode in ambfor 2075 upto 330 flexible atoms. 2076 2077- Molden reads back in ambfor .xyz files better. 2078 2079- Updating labels no longer lags in slow connection opengl mode. 2080 2081- Resizing main screen in opengl is now one update. 2082 2083Tue Jul 7 2084 2085- Added the possibility of partial optimisation. If you want to optimise 2086 a docked pose, select only the ligand and the surrounding residues 2087 flexible. And optimise with the the amber/gaff force field. 2088 2089- Molden now supports the scroll wheel to zoom in and out. 2090 2091- When using starnet X-Win32 X-windows server, gmolden switches 2092 to use full OpenGL (not mixed xwindows/opengl mode). 2093 The newer versions of X-Win32 ver 8, have problems with 2094 zooming in via the Ctrl key, in this case use the right Control key 2095 or the scroll wheel. 2096 2097- Molden can not determine which version of X-Win32 server is active. 2098 You can use the molden commandline flag -Q, to return to the mixed 2099 OpenGL/Xwindows mode. This will work better with older versions of 2100 X-Win32 (6.1 and older). 2101 2102- When aligning two small molecules and using the align and combine 2103 option, there was an extra copy of one of the molecules. Fixed it. 2104 2105Wed Jun 3 2106 2107- Removed bug from the handling of the multi mol2 and sdf files 2108 2109Fri May 28 2110 2111- Added the option to compile a complete GL version of gmolden. 2112 Uptill now gmolden did some graphics in xwindows and most graphics 2113 in OpenGL. In the MacOSX version of gmolden, the xwindows graphics 2114 were not visible. I therefore created the option to let gmolden 2115 do all graphics with OpenGL calls. You request this new functionality 2116 by adding the -F command line flag. 2117 2118Mon May 4 2119 2120- fixed annoyance that during animations, the animation would stop because 2121 of the help window popup on the button started the animation. 2122 2123Tue Apr 28 2124 2125- fixed bug that could screw up the displaying of secundary structure 2126 in the opengl version of molden, in the case of multiple proteins 2127 being loaded. 2128 2129Mon Apr 27 2130 2131- Multi molecule files, such a .sdf files and .mol2 files will now 2132 open an extra window in which each separate molecule is clickable. 2133- In addition you can now combine .mol2 files conataining poses for 2134 a ligand with the protein being docked into: 2135 First load protein. Second, read multi mol2 file with "Add" selected 2136 in the read file window. 2137 2138Wed Apr 16 2139 2140- added the calculation of topological polar surface area (PSA). 2141 Molden control window -> surface icon -> totpol. PSA 2142 2143- added the calculation of the Quantum Mechanical PSA, 2144 fisrt calculate a 3dgridfile with the density, second calculate 2145 3dgridfile with QM electrostatic potential (slow), 2146 Start up molden, go to the density mode, read in density gridfile 2147 map esp on density, Vr icon. -> mapped 2148 2149- fixed bug, after animating normal modes going into the zmatrix 2150 editor, clicking one of the variables would move the structure 2151 allow a normal mode. 2152 2153- added the reading of multi molecular sdf files. 2154 click the 'M' button to select other structures in the sdf file 2155 2156- fixed a bug that would mess up windows on centos, when keeping 2157 the pointer over a button and make the help text appear. 2158 2159 2160Thu Mar 5 2161 2162- fixed bug causes the atoms not to be connected in the density mode 2163 in combination with gamess-us and qchem outputs 2164 2165- fixed a bug that would shown an empty structure for orca outout. 2166 2167- surface off would sometimes also switch off some parts of the coil 2168 in opengl mode; fixed it 2169 2170Wed Feb 25 2171 2172- MAYOR: BUG FIX FOR AMBFOR the standalone amber/gaff force field 2173 optimizer which is called by molden. 2174 The bug caused some torsion force constants to be to big and 2175 could lead to distorted optimised geometries. 2176 eg anything with a -so4- group. 2177 2178- fixed a bug that would let molden crash when deleting all active structures 2179 from the structures window, when the atom attributes window was displayed. 2180 2181- some programs out there write pdb files with lowercase element and residue 2182 labels. Molden can now handle these. 2183 2184- fixed a bug that caused read in ambfor .xyz files, to be treated as 2185 if they had no charges 2186 2187Thu Jan 15 2188 2189- added 64 bits executables for linux on our anonymous ftp directory 2190 ftp://ftp.cmbi.umcn.nl/pub/molgraph/molden/bin/Linux/64bits 2191 2192- fixed a minor bug in the 64 bits version when rendering helices 2193 2194The Dec 18 2195 2196- Zoom is now kept when editing a zmatrix 2197- Updated the makefile somewhat, let me know if you have problems with it 2198 2199Tue Nov 25 2200 2201- When a protein was edited via the z-matrix all waters were gone 2202 except those with a connection to the protein. Now the waters are 2203 restored when exiting the z-matrix editor. 2204 2205- removed a a bug in an earlier undocumented implementation of the 2206 above that would make molden crash during the animation of variables 2207 in the z-matrix editor. 2208 2209Thu Nov 20 2210 2211- Added the posibility to color by chains (opengl only). 2212- fixed a bug that would render the molecule as opengl sticks after 2213 a HETATM molecule of a protein was removed via the 2nd mouse click 2214 popup window. 2215 2216Wed Nov 12 2217 2218- fixed a bug that could make molden freeze when a help window on a 2219 button was activated 2220- fixed a bug with rendering forces and the in/de-crease scale buttons. 2221- fixed a small bug with reading non protein mol2 files, which would cause 2222 problems when combining the molecule with a protein structure. 2223- Fixed bug which caused crystal information (biosym car,arc), to be 2224 wrongly symmetry expanded if it was not the first structure be read in 2225- fixed a bug that would let molden crash when clicking H-BONDS in the 2226 stick mode 2227- fixed a bug that would let molden hang on reading a VASP CONTCAR file 2228- fixed a bug that would let molden crash when as a first file a freq 2229 jobs was read in, and consequently the spectrum was displayed. 2230 (introduced very recently). 2231 2232Mon Nov 10 2233 2234- Fixed bug in memory allocation associated with the writing of .ogl 2235 files in the surfaces window. 2236 When you do a combine between a small molecule and a protein, the memory 2237 would be corrupted. fixed it. 2238 2239Fri Nov 7 2240 2241- Fixed bug writing "charges derived" electrostatic potential mapped 2242 surfaces in opengl surfaces window 2243 2244- Fixed minor bug in writing mopac surfaces in density mode in 2245 opengl surfaces window 2246 2247Thu Nov 6 2248 2249- Fixed bug which caused filetypes with crystal information (biosym car,arc) 2250 and multiple structures to be treated as containing just one structure. 2251 2252- when only surfaces but no molecule was present in a .ogl, 2253 the scene would not be properly displayed. In perspective mode 2254 you would be inside the surface with no possibility to zoom in. 2255 In the non-perspective mode nothing would be displayed. 2256 Fixed it. 2257 2258- fixed bug in new .ogl writing routine, that sometimes wrote too many 2259 connections. 2260 2261Tue Nov 4 2262 2263- when choosing contacts to be displayed followed by a distance 2264 measurement, the part of the distance window where the distance 2265 should be displyed stayed black, fixed it. 2266 2267- in pdb files with dna/rna the label OP2,OP1 where not supported, 2268 now they are. 2269 2270Fri Oct 31 2271 2272- The newly introduced surfaces window also now allows to write all 2273 surfaces to a .ogl file. You can for instance now create several 2274 orbitals and write then to a .ogl file 2275 2276- .ogl files ca now be read back in to gmolden. 2277 2278Fri Oct 24 2279 2280- A new window lets you manage the opengl surfaces created by molden. 2281 In the molden control window -> color palette icon -> surfaces 2282 You can delete surfaces, change color. Separate helices can now 2283 be colored differently. The surfaces window is also available in 2284 the denisty mode. It automatically pops up once the opengl icon 2285 is clicked. Surfaces can now be activated and deactivated. 2286 2287- The .ogl files when selected in the read file window used longer 2288 trigger the launch of the external moldenogl helper program. 2289 This behaviour still goes for the Xwindows only version of molden. 2290 For the mixed opengl/Xwindows version of molden (gmolden), the .ogl 2291 files are dispayed within gmolden itself 2292 2293- Removed a bug that would overwrite the last read file with postscript 2294 code, when the character 'p' was pressed in the display window of 2295 molden. 2296 2297Wed Sep 17 2298 2299- The align button in the structures window now also works for small 2300 molecules. 2301 2302- When viewing gromacs trajectory the backbone view is maintained if 2303 chosen. Also the labels of the cell are no longer displayed in this case. 2304 2305- You can now create a separate structure from the pdb hetatm molecules 2306 by clicking with the 2nd mouse button on the drawing screen. 2307 This makes it easy to save these molecules in a separte pdb file. 2308 2309- Added cyclopentane and pyrrole as fragments in the zmatrix editor. 2310 2311Fri Sep 12 2312 2313- Added the option to map the electrostatic potential to the solvent 2314 accessible surface 2315 2316Tue Sep 9 2317 2318- Added the possibility to align proteins 2319 2320Fri Aug 29 2321 2322- Removed another bug that made the program crash when freeing allocated memory 2323 2324Thu Aug 28 (My birthday :-) 2325 2326- Removed a bug that made the program crash when freeing allocated memory 2327 2328- mol2 files containing multiple structures are now also supported. 2329 An extra button (M) in the points section of the molden control window 2330 will appear. Clicking this button will allow you to select an other 2331 structure in the mol2 file. 2332 2333- Two structures can now be combined. Select a structure, supply a 2334 structure number in the field next to the "Combine" button, and click 2335 'Combine'. The structure corresponding to the number will be appended 2336 to the active structure. 2337 2338Molden 4.7 first version Aug 22 2008 2339 2340- Molden4.7 can keep multiple structures in memory. Each time a new file is 2341 read in this is a new structure. You can switch betweeen structures 2342 in the newly added structure window. The currently selected structure 2343 is displayed. You can also delete structures in this window. The original 2344 one structure at a time behaviour is still available when specifying 2345 the -O command line flag. 2346 2347Molden 4.6 2348 2349Tue Aug 12 2350 2351- Fixed a bug when going up one directory (..) in the filemanager. 2352 This one managed to escape my attention for a long time. 2353 2354- Minor changes to scrolling 2355 2356Wed Jul 6 2357 2358- Added dynamic memory allocation voor mopac2007 .aux files 2359 2360Wed Jul 2 2361 2362- Removed a bug that lets molden crash when you add the first line 2363 of a new structure in the z-matrix (windows,macosx) 2364 2365Tue Jun 24 2366 2367- The mopac2007 .aux format is now supported. 2368 The mopac .aux format can hold geometry optimisation data, charges, dipole 2369 and orbitals information. 2370 The MP6 and RM1 methods have been added in the submit job interface. 2371 2372- Corrected a bug in displaying the dipole moment. 2373 2374Thu May 29 2375 2376- Activating the picture icon will allways cause a gif image to be 2377 written, also in OpenGL mode. The latter requires a 24 bit to 8 bit 2378 conversion, which has now been incorporated into molden. 2379 For those who would like the rgb picture back, let me know. 2380 2381Tue Apr 29 2382 2383- Removed bug in gmolden that when adding the first atom in a new 2384 z-matrix would make the atom invisible (solid/stick mode only). 2385 2386- Added the ability to cap residues 2387 2388- Added support for neutral asp, glu and lys (ambfor force field) 2389 2390- Improved zmatrix editing of proteins: adding H to histidine will 2391 now be recognized as the proper HIS form. 2392 2393Wed Apr 16 2394 2395- Small annoyance fixes. 2396 Switched atom selecting back to the fisrt mouse button again in the 2397 atom properties windows. 2398 When doing a optimisation, selected atoms now become unselected. 2399 2400 2401Thu Apr 3 2402 2403- Added small help boxes describing the use of button. If you keep the pointer 2404 over a button and dont move, after 1.5 seconds, this helpful window 2405 will appear. NOT yet implemented for all windows !! 2406 Gradually help for more windows will be added. 2407 2408- Added possibility to close/abort query box 2409 2410- When the user would try to kill the main drawing window by clicking 2411 on the x in the border supplied by the window manager, molden would popup 2412 a window saying you should kill molden by clicking on the skull button. 2413 On some Xwindow servers, this popup window would be off screen. Fixed it. 2414 2415Tue Mar 18 2416 2417- In the window to specify the atoms and methods for Oniom, the possibility 2418 of writing amber charges as part of the element specification for Gaussian 2419 has been added. 2420 2421Fri Mar 14 2422 2423- While reading tinker/ambfor xyz files, a proline could be misclassified 2424 as a lysine. The most visible direct effect was strange behaviour of 2425 the spline to indicate the coil secundary structure. 2426 Fixed. 2427 2428Thu Mar 13 2429 2430- Labels of Cell axes are now also visible in the opengl mode of gmolden. 2431- Labels of XYZ axes are now also visible in the opengl mode of gmolden. 2432 2433Mon Mar 10 2434 2435- Fixed bug in 'edit cell parameters' 2436 2437Fri Feb 22 2438 2439- Added axes, only in gmolden with solid mode. It can be called by pressing 2440 '+' or '='. No labels of axes yet: red=x, green=y, blue=z 2441 2442- Added the possibility of calculating molecular surfaces, with help of the 2443 program 'surf': 2444 2445 ``Linearly Scalable Computation of Smooth Molecular Surfaces", 2446 A. Varshney, F. P. Brooks, Jr., and W. V. Wright, IEEE Computer Graphics 2447 and Applications, September 1994 [invited submission]. 2448 2449 You will find the option under the 'surface' icon -> Mol. surf. 2450 This option is mainly intended for use with proteins. 2451 2452Fri Jan 25 2453 2454- corrected bug in reading molden format files when non integer occupation 2455 numbers would be present. 2456 2457Mon Jan 21 2458 2459- Added reading/writing of CIF files 2460 2461Thu Jan 10 2462 2463- Added writing of Gaussian cube files (reading was already present). 2464 This can also be used to store data on a 3D grid which are slow to 2465 calculate. 2466 2467Mon Dec 17 2468 2469- fixed a bug which could make the automatic z-matrix conversion crash 2470 for very small molecules with few connected atoms 2471 2472Wed Dec 12 2473 2474- Fixed working with nptsx,nptsy,nptsz, edy,edy,edz in combination 2475 with opengl 2476 2477- Going to full screen in OpenGL mode would leave the molecule not 2478 centered on the ceter of the screen, fixed it. 2479 2480- Refined creating connections between backbone connections. 2481 2482- Refined handeling of unclassified pdb symbols in the ATOM records 2483 of a PDB file. 2484 2485- Fog is now automaically disabled in the density mode. 2486 2487Mon Dec 10 2488 2489- Fixed atom selection by clicking on an atom with the second mouse button 2490 while the "Atom Properties window" is open. This functionality was 2491 destroyed when introducing the popup window for HETATM molecules on 2492 Aug 8 2493 2494Fri Dec 7 2495 2496- Atomcolor is now switch on for all but protein structures after 2497 reading a new file 2498- Better default setting of shade for proteins 2499 2500Sat Dec 1 2501 2502- Fixed Molden in such away that it is more compatible with the free 2503 Xming Xserver for windows. 2504 2505- Fixed a bug that would let the structure rotate after an buttonpress 2506 in the main screen and clicking on of the amino acid options. 2507 2508Fri Nov 23 2509 2510- fixed bug with displaying G-functions 2511 2512Wed Nov 14 2513 2514- Added optimisations for displaying the opengl stick & balls for all atoms 2515- added support for gaussian counterpoise optimisations. 2516- added a commandlineflag -S to let molden start with shade off. 2517 2518Fri Nov 9 2519 2520- Added support for gaussian mp2 optimisations 2521 Previously the HF energy would be listed in the geometry convergence 2522 window, now the MP2 energy will be displayed. 2523- Added support for gaussian IRC outputs, previously all points were displayed 2524 in the geometry convergence windows, now only the optimised geometries 2525 along each point of the reaction coordinate. 2526 2527Wed Nov 7 2528 2529- added a window that lets you specify the total charge when using 2530 the EEM charges. 2531- added two new parameter sets to calculate EEM charges with, PESP and 2532 ESFF force field parameters 2533- Changed the default for automatically calculating charges for forcefield 2534 optimisation with ambfor to PESP. This is because the previous default 2535 only had parameters for HCNOF. In addition a string will be printed 2536 when no parameters for an element are available. 2537 You can always assign charges interactively and switch off automatic 2538 charge assigning in the AMBFOR optimise window. 2539- Improved GAFF forcefield typing a bit. 2540- Removed a bug that would occasionally make molden crash when doing a 2541 interactive GAFF/Ambfor optimisation and charge labels were also printed 2542 (Recursive IO bug). 2543- when the number of atoms exceeded 10000 the writing of tinker xyz files 2544 would not print connectivity correctly, fixed it. 2545 2546 2547Tue Oct 30 2548 2549- added option to interactively change the parameters that determine 2550 when molden draws a hydrogen bond. You will find a new entry 'H-bond 2551 parameters' under the H icon, the 8th icon from the top from the 2552 middle column in the molden control window. 2553 2554Tue Oct 23 2555 2556- fixed a bug where the reading of Gaussian files would go wrong if 2557 the following line was present: 2558 2559 RelInt: Using uncontracted basis, .... etc. 2560 2561Wed Oct 17 2562 2563- added a 'prev' button in addition to the existing 'first', 'next' and 2564 'movie' buttons. 2565- added to molden makefile, the feature to build molden, gmolden and 2566 ambfor/ambfor when you type 'make' 2567- added option to convert gaussian log files to zmatrices: 2568 2569 gmolden molin 2570 2571 contents of file molin: 2572 title 2573 file=gaussian.log wrzmat=2 2574 2575 The zmatrix will be written in the file called 'zmat.out' 2576 2577- added possibility to scan a part of a proteins rotamer space 2578 (max. 6 residues). The best 10 rotamer combinations will be remembered. 2579 The initial scoring is done via the dfire pmf score. The output can 2580 be saved and (re)loaded via the file 'resrot'. The rotamer combinations 2581 can be rescored with the amber force field. 2582 To activate the window click on a residue with the second mouse button 2583 and select the last option in the menu (add flexible residue). 2584 Subsequently do the same for all the residues you want to be flexible. 2585 However you first have to create a zmatrix for the protein fisrt by clicking 2586 the zmatrix button, otherwise the new option will not be presented. 2587 2588Thu Sep 13 2589 2590- Fixed bug when applying edited cellparameters 2591- Added option to calculate charges for hetatm molecules from the PDB 2592 (in the popup menu, activated with second mouse button click) 2593 2594Fri Sep 7 2595 2596Fix bug ambfor memory allocation 2597 2598Mon Sep 3 2599 2600Fixed bug that caused the zmatrix-ordering of atoms to be applied 2601without also changing the charges ordering accordingly, when 2602starting an ambfor (amber/gaff) optimisation. 2603 2604Thu Aug 30 2605 2606Fixed bug when writing zmatrices bigger than 100 atoms. 2607 2608Wed Aug 29 2609 2610- improved GAFF typing 2611 2612Thu Aug 23 2613 2614- fixed a bug that would not display a residue when replaced (in opengl) 2615 2616- fixed a bug that could occur when memory is allocated for proteins 2617 larger than 20000 atoms. 2618 2619Fri Aug 17 2620 2621- fixed bug that displayed "(null)" string when the cursor was above 2622 an atom when displaying a non pdb file 2623 2624Tue Aug 14 2625 2626- fixed a bug that caused molden not to make a correct z-matrix for 2627 a pdb file containing nucleotides 2628 2629Wed Aug 8 2630 2631- added support with ORCA through reading of the ORCA output, currently 2632 supported are: 2633 2634 single point, geometry optimisation and force/frequency jobs 2635 2636 No support for reading electron density and orbitals 2637 2638- Added support for hetatm moelcules from the pdb file, which label 2639 will now light up when the pointer is over the hetatm molecule. 2640 Clicking the middle mouse button will now bring up a popup menu 2641 with options to center on the molecule, create a surface of the 2642 molecule and to find neighbouring aminoacids. 2643 2644Mon Jun 11 2645 2646- Fixed bug in displaying residue labels for pdb files containing DNA 2647 2648- Added the option to have a background color with a gradient. 2649 When clicking the 'Palette' icon the first option now is 'Background Mode' 2650 You can choose between "solid color" (the way it was) and ' color gradient' 2651 To implement this we changed color 13 of the 15 basic molden colors to dark 2652 blue, which is used for the default gradient color. 2653 Of course this affects the .moldenrc file so you had best remove it and 2654 reset your defaults. The background mode is also saved in the .moldenrc 2655 file. 2656 2657- Added the reading of electron density maps in the O format (also known as 2658 DSN6 format) these are available form the electron density server in Upsala: 2659 2660 http://eds.bmc.uu.se/eds/ 2661 2662 These maps are only displayed in the OpenGL mode (so gmolden). 2663 2664Wed May 30 2665 2666- Fixed a bug in writing .mol filee, of elements with a two letter abbreviation 2667 only the last was written. 2668 2669- added reading of DSN6 electron density maps, these can be read in from 2670 the surface icon -> last option and can be displayed on top of a pdb 2671 structure 2672 2673- added information how to compile under gfortran/gcc4.0 and higher to 2674 the makefile and molden.f file (uncomment external gfortran_iarc) 2675 2676Fri May 4 2677 2678- Fixed bug of displaying the dipole moment, the dipole moment 2679 was only correctly displayed for single point QM calculations, not 2680 QM optimisations. Fixed it. 2681 2682Tue Mar 20 2683 2684- Removed a bug affecting the processing of biosym .car files. 2685 Bug was introduced when adding dynamic memory allocation for protein 2686 coordinates 2687 2688- Removed a bug affecting reading of xyz files being added to an existing 2689 structure. 2690 Bug was introduced when adding dynamic memory allocation for protein 2691 coordinates 2692 2693Mon Mar 12 2694 2695- Removed a bug affecting the visualisation of vibrations of gamess-us 2696 and Qchem introduced when adding dynamic memory allocation for protein 2697 coordinates 2698 2699Fri Mar 9 2700 2701- Removed a bug in the processing of gaussian outputs, the bug is 2702 'fixed' but be aware that it is not exhaustively tested as of yet 2703 2704- made a minor bug fix to the reading of QChem output 2705 2706Fri Mar 2 2707 2708- Performance update: OpenGL density mode now makes less unnecessary 2709 screen updates. Only important for working with remote displays. 2710 2711Tue Feb 20 2712 2713- Created dynamic memory allocation for proteins (all formats that support 2714 protein information, pdb, mol2, tinker xyz, .gro) 2715 2716- Display of dipole moment, if QM electron density is available, the QM dipole 2717 moment is first calculated, if charges are available (but no QM electron 2718 density), the dipole moment is calculated from the charges. 2719 2720- Added possibility to rotate ligand within an active site: 2721 2722 The align icon (middle column, 9th from the top) Interactive docking -> 2723 Pick molecule from screen -> pick a molecule from the HETATM records of 2724 the Pdb file. 2725 2726------------------------------------------------------------------------ 2727 2728Molden 4.5 2729 2730Fri Dec 2 2731 2732- Optimised protein display in the opengl version: 2733 2734 - residues now have their own gllist, when you display a whole 2735 protien as solid you will see the protein being build up residue 2736 per residue. Solid protein display will also display somewhat faster. 2737 - when clicking the backbone button you will immediately see the 2738 secondary structure elements 2739 - animation of variables in the zmatrix editor in solid mode will 2740 be a lot faster, also replacing rotamers. 2741 - you can now choose between the richardson and dunbrack rotamer 2742 libraries 2743 2744Tue Oct 17 2745 2746- Did some improvements to the QChem interface 2747 2748Thu Sep 7 2749 2750- Did some optimisation of orbitals and regular density space filling 2751 plots. 2752 2753Thu Aug 31 2754 2755- changed the fortran code so that use of the -O2 compiler flag on linux 2756 nolonger causes incorrect display of the surface in xwindows lines mode 2757 (the surface looked incomplete) 2758 2759Thu Aug 17 2760 2761- The opengl version of molden (gmolden) would show dark blue lines 2762 in the density-3dgrid mode with certain xwindow emulators. Fixed it 2763 so that the lines are white again i 2764 2765Wed Jul 12 2766 2767- added a button "to Xmgr" which when clicked will right a file with 2768 pairs of frequency,intensity on each lines. These files can be imported 2769 into xmgr or xmgrace 2770 2771Mon Jul 10 2772 2773- when displaying vasp POSCAR or CONTCAR files, and there is a XDATCAR 2774 file present molden will ask to use the XDATCAR, the multiple structures 2775 can be called with the 'fisrt','next' and 'movie' buttons. 2776 2777- when doing interactive docking sometimes extra hydrogens were added 2778 to the second molecule with erroneous connections to the first molecule, 2779 fixed it. 2780 2781- when doing interactive docking you are now asked if you want to align 2782 the centers of both molecules or not (yes used to be the default) 2783 2784- the make option 'make noxwin' now should work again. This can be used 2785 to create a version of molden without xwindows and opengl, you can 2786 only control this version with a keyword file. 2787 2788Wed Jun 28 2789 2790- The internal opengl representation of mopac .gpt files had errors 2791 in representing the connections of the molecule. 2792 2793- Tinker xyz files which use the amber or charm forcefields are now 2794 correctly visualized when atoms like F, P Cl and Br are used. 2795 2796Tue Jun 6 2797 2798- B. van Eijck added the keyword CHADD, which will read extra charge 2799 centers from a 'molden.def' file. 2800 2801Tue May 30 2802 2803- Removed some small bugs, reported by Robert Gyepes 2804- added a special makefile for cygwin makefile.cygwin 2805 2806Fri May 19 2807 2808- Added 'best rotamer' option, this calulates for a particular residue, 2809 the best scoring rotamer according to the dfire protein-protein score. 2810 2811- Removed a bug which on some platforms would make molden crash when 2812 writing out a z-matrix 2813 2814- Some rudumentary support for gfortran (you still have to edit molden.f 2815 and comment out the line 'external iargc' ) 2816 2817Wed Mar 8 2818 2819 Spherical G-functions (9G) in combination with electrostatic potential 2820 and mulliken charges are now also fully supported 2821 2822Mon Mar 6 2823 2824- Support for Gaussian cartesian G-functions (previously i was unaware of 2825 G-functions in the Gaussian series of packages). 2826 2827- Support for the Gaussian03 revision D, the output format of the basisset 2828 has slightly changed. Adpated molden to deal with it. 2829 2830 2831Tue Feb 7 2832 2833- First support for QChem outputs: For molden to be able to read orbital 2834 and basis-set information, supply the following qchem keywords in the $rem 2835 section: 2836 2837 PRINT_ORBITALS TRUE 2838 PRINT_GENERAL_BASIS TRUE 2839 2840 You can supply output of composite qchem jobs, molden detects it and will 2841 allow you to select the different job outputs by clicking on the 'M' button 2842 which appears in the "Select Point:" section in the molden control window. 2843 2844 NOTE: support is still rudimentary, i dont have qchem, only a few outputs 2845 sent to me by a user. If you think this functionality is important 2846 than let me know when it doesnt work 2847 2848Thu Jan 19 2849 2850- Support for dynamic memory allocation for the part that shows geometry 2851 convergence, implemented for use with gromacs and cpmd. 2852 2853- In popop menus you always had to choose a selection (sometimes cancel) 2854 Now you can click besides the popup window to get out of the popup and 2855 cancel the selection. Therefor the option "Cancel" there where used to 2856 be offered has been removed. 2857 2858Tue Dec 20 2859 2860- Support for the latest Gamess-US version (tested 27 JUN 2005 (R3) version). 2861 The basis-set print out of Gamess-US version had changed. 2862 2863Fri Dec 16 2864 2865- When writing PDB files, in case of no chain information read in 2866 molden will now generate and write chain labels 2867 2868- With gromacs files the generation of connectivity is now much quicker 2869 also solvent molecules will be rendered in less detail in opengl molden 2870 which will speed things up a little 2871 2872Fri Dec 9 2873 2874- Molden can now read the binary gromacs files .trr and .edr. Previously 2875 molden would first convert them to their ascii counterparts with the gmxdump 2876 utility. This way the very large ascii files are nolonger needed. 2877 2878Tue Nov 29 2879 2880- Added molden keyword 'MOGL' which will let you create a molden.ogl 2881 file from a molden keyword file. 2882 2883Mon Nov 28 2884 2885- When replacing one amino acid residue by another, followed by writing 2886 a pdb file, the replaced residue number would be wrong: fixed 2887 2888- When writing .mol2 files, sometimes a double bond to many was written 2889 (conjugated systems), since molden does not do anything with bond types 2890 this was not serious, but other programs (sybyl) do work with bond types. 2891 2892- When Cbeta or backbone O (C=O) was missing on a pdb residue, connections 2893 to a non existing atom at cart.coord (0,0,0) would be drawn in the opengl 2894 version of molden (gmolden) 2895 2896Mon Nov 7 2897 2898- With gmolden the aminoacid currently under the pointer is shown by 2899 temporarily showing the label, when clicking with the second mouse button 2900 a popup window with a few options pertaining to amino acids would appear, 2901 every now and then this window would not be visible untill you moved the 2902 pointer over it (only on certain xservers), fixed it. 2903 2904Wed Nov 2 2905 2906- Fixed writing of Gaussian inputfiles for oniom calculations (from the submit 2907 Gaussian Job windows). This bug was introduced when charges for proteins 2908 were added (amber forcefield) in molden4.1 (Why does no one ever tell 2909 me it does not work ???) 2910 2911- Changed the working of the residue commands window: 2912 2913 128-130:A would mean residue 128 through 130 of chain with Label "A" 2914 2915 NOW all numbers refer to residue numbers used in the PDB file: 2916 128-130:A now actually means the same as 128-130. 2917 You still can use the chain label for things like coloring: 2918 2919 *:A col 2920 2921 Will let you pick a color with which all residues belonging to chain "A" 2922 are colored with this color 2923 2924 128 2925 2926 residue with PDB residue number 128 will be shown. 2927 2928 2929 2930Fri Oct 28 2931 2932- fixed a bug that would override user assigned sybyl atom types, when 2933 writing mol2 files 2934 2935- added the possibility to change the potential levels at which certain colors 2936 where used for the colorcoded opengl esp potential 2937 2938- The PC-UNIX version of Gamess-US misses the first column with respect 2939 to the regular Unix version, made some adaptation to let molden work 2940 with this output to. 2941 2942- Fixed geom conv for a series of xyz structures where so of them had 'heat' 2943 0.0 2944 2945 2946Fri Sep 30 2947 2948- reorder Z-matrix, clicking a few atoms and then hitting 2949 escape, this would create a zmatrix in the order of clicked atoms 2950 and the rest would be figured out by molden. This did not always 2951 work. I fixed it in such a way that it can handle nearly all cases 2952 but there are still some conditions not supported, but this is not 2953 so relevant since you can always do it again. 2954 2955- When doing interactive docking, you can now change the center around 2956 which the ligand rotates (in the same way as the overall rotation center). 2957 And you can now reorder the z-matrix of the docked ligand. 2958 2959Wed Sep 23 2960 2961- Added the possiblity to do a surface per residue in the surface window 2962 (opengl version only), takes longer but also looks a lot better. 2963 2964- When aligning or docking and then writing as a PDB file some of the atoms 2965 were missing, corrected it. 2966 2967- When docking a molecule, the to be docked molecule is placed at the center 2968 of the molecule docked to. 2969 2970Wed Sep 21 2971 2972- Fixed running tinker in the background for the opengl version of molden 2973- Made residue commands concerning surface also work for the opengl version 2974- Added Fit Rotamer option, which will replace the amino acid conformation 2975 with the closest rotamer in the rotamer library 2976 2977Mon Sep 5 2978 2979- Added support for the tinker amoebapro force field 2980- reading in tinker xyz amber files would be retyped to charmm types 2981 fixed this 2982 2983Mon Aug 15 2984 2985- Fixed xwin.c for molden without OpenGL 2986 2987- Fixed writing of GIF files for using Xservers with 16 bit planes 2988 2989Fri Jul 15 2990 2991- Added interactive opengl support for the density mode (only available 2992 with 'make gmolden'). 2993 2994- Fixed bug which can lead to not displaying gaussian outputs correctly 2995 in some cases. 2996 2997- Fixed a number of small annoyances (dont worry, there are enough left). 2998 2999 3000Wed Jun 15 3001 3002- fixed bug that let f-functions run in to the code meant for the g-functions 3003 resulting in reporting number of orbitals is wrong 3004 3005- fixed reading MOL files, this bug was introduced with support for reading 3006 gromacs files 3007 3008Thu Jun 2 3009 3010Addition of creating opengl surfaces in the molecular mode, when clicked 3011add to the backbone (protein structure only), and clicking with the second 3012mouse button on a backbone atom a drop menu will appear, which let you 3013do things like (un)display the residue, center it, and add to the surface 3014(of course only available when molden is compiled with opengl support (gmolden)) 3015 3016------------------------------------------------------------------------ 3017 3018 Molden4.4 3019 3020Mon May 9 3021 3022The main reasons for this new minor version of molden are: 3023 3024- Introduction of the incorporation of interactive Opengl in the main 3025 interface of molden (molden already had opengl helper program moldenogl) 3026 You can build the gmolden version by typing; 3027 3028 make gmolden 3029 3030 This version is still under development 3031 3032- Reading of NLMO's of the NBO analysis in gaussian 3033 3034- Partial support for G-functions. As far as orbitals and electron density 3035 G-functions are supported. Also mulliken charges, except when using 9G 3036 functions. The electrostatic potential is not yet supported. 3037 3038 Addition of a new keyword to the molden format: [9G] 3039 3040 which specifies the use of spherical G-functions instead of gaussians. 3041 3042 The order in which molden expects MO coefficients to pe printed is: 3043 For spherical G-functions: 3044 3045 G 0,G+1,G-1,G+2,G-2,G+3,G-3,G+4,G-4 3046 3047 For cartesian G-functions: 3048 3049 xxxx yyyy zzzz xxxy xxxz yyyx yyyz zzzx zzzy 3050 xxyy xxzz yyzz xxyz yyxz zzxy 3051 3052 The request for support for G-function came from the molcas development 3053 people, but also Gamess-US will benefit from this support. 3054 3055------------------------------------------------------------------------ 3056 3057 Molden4.3 3058 3059Fri Apr 29 3060 3061- introduced number of small bug fixes: 3062 the environment g03root was not recognised and g98 was written in the 3063 .run files created by molden 3064 3065- premature end of file in gaussian can let molden crash, removed one 3066 instance on which it could crash 3067 3068- Introduction of the incorporation of interactive Opengl in the main 3069 interface of molden (molden already had opengl helper program moldenogl) 3070 You can build the gmolden version by typing; 3071 3072 make gmolden 3073 3074 This version is still under development 3075 3076- Reading of NLMO's of the NBO analysis in gaussian 3077 3078- addition of dynamic aminoacid labels and clicking on a backbone 3079 atom will bring up a small dropdown menu with visualisation options 3080 3081Wed Feb 23 3082 3083- Fixed bug that effectively disabled the aligning of two molecules 3084 3085- Fixed a bug in the z-matrix editor that would not correctly show all 3086 atoms in the when the 'stickcolor' mode was disabled. 3087 3088Fri Jan 28 2005 3089 3090- Lots of small bugfixes, as there are: 3091 3092 Fixed editing z-matrix of ligand when doing interactive docking, 3093 Not edit operations where bug free 3094 3095 Fixed updating of properties when editing the z-matrix 3096 3097- Added support for the Gromacs (gmx) file format .gro: 3098 3099 Molden will read the file name.gro and will then look for the file 3100 name.top to read connectivity, charges and atom types. When not found 3101 Molden will create connectivity. 3102 3103 Next molden will look for a trajectory file name.ttr. If found it will 3104 use gmxdump to convert it to an ascii trajectory file name.trra. 3105 Molden will not do the conversion if a ascii trajectory file name.trra 3106 already exists. 3107 3108 Next molden will look for an energy file name.edr. If found it will 3109 use gmxdump to convert it to an ascii energy file name.trra. 3110 Molden will not do the conversion if a ascii trajectory file name.trra 3111 already exists. 3112 3113 If a trajectory file is found, then molden can animate the MD run by 3114 clicking on the movie button. 3115 3116- Hitting the escape key when running an animation will exit the animation. 3117 Hitting the space key will stop the animation and when hit again will resume 3118 the animation. 3119 3120Fri Jan 14 2005 3121 3122- Some more work on the writing of mol2 file for proteins. 3123 3124- Incomplete amino acids are now reported. 3125 3126- changed xwin.c so it does better on 64 bits AMD/Opteron systems. 3127 3128Tue Dec 21 2004 3129 3130Introduction of Molden4.3: 3131 3132- The reading of Gaussian output files has been restructured, it is 3133 possible that this may temporarily be a step back in molden reliablity. 3134 PLEASE inform us of any problems related to reading gaussian outputs. 3135 3136- Did some work on writing better mol2 files for proteins, there are 3137 still problems, but at least molden can now read it back and create 3138 a z-matrix for the protein without crashing. 3139 Sybyl still has problems with these files ! It needs more work. 3140 3141- Added forces information to the molden format, example: 3142 3143 [FORCES] 3144 point 1 3145 3 3146 -0.000038 -0.000160 0.000430 3147 0.000834 0.000150 0.000047 3148 -0.000263 0.000008 -0.000017 3149 point 2 3150 3 3151 -0.000505 0.000339 0.000987 3152 0.001268 -0.000634 -0.000242 3153 0.000123 -0.000017 -0.000640 3154 .... 3155 point 10 3156 3 3157 -0.001299 0.000970 0.001904 3158 0.002139 -0.001328 -0.001049 3159 0.000512 0.000004 -0.001636 3160 3161 The number of points must match the number of points used in the [GEOMETRIES] 3162 section. 3163 Second form includes coordinates, this is only needed when the forces are 3164 not in the same orientation as the geometries supplied in the [GEOMETRIES] 3165 section. For instance, the Gamess-US forces are not in the z-matrix orientation 3166 , so when [GEOMETRIES] ZMAT is used the forces would not be in the correct 3167 orientation. 3168 3169 [FORCES] COORD 3170 point 1 3171 3 3172 -0.000038 -0.000160 0.000430 0.0 0.0 0.0 3173 0.000834 0.000150 0.000047 0.0 0.0 1.0 3174 -0.000263 0.000008 -0.000017 0.0 0.0 -1.0 3175 .... 3176 3177 NOTE: this extension is on trial, it may not be the final solution. 3178 Developers who write their own molden format should not be 3179 overanxious to implement it. 3180 3181 - fixed problems with reading circulair peptides. 3182 3183 - increased the max number of geometries and scf iterations molden can handle 3184 to 2000 and 1000 respectively. 3185 3186------------------------------------------------------------------------ 3187 Molden4.2 3188 3189Tue Oct 05 2004 3190 3191- Corrected a few fortran syntax errors, thnx to Gyepes R. 3192- on some platforms molden would not write a z-matrix, after stating 3193 that it just did. fixed 3194 3195Thu Aug 05 2004 3196 3197Molden 4.2 introduces quite some radical changes in the way proteins 3198can be manipulated with the z-matrix editor. Where in previous versions 3199any change to the z-matrix was followed by a complete update of the 3200cartesian structure, with molden4.1 only those parts of the cartesian 3201structure are updated that have actually changed. 3202The advantages are that protein manipulation is much faster and now 3203larger proteins can be manipulated, these manipulations include, 3204deletion, insertion and replacement of amino acids. Also the animation 3205of variables such as the chi sidechain rotamer angles can now be done 3206interactively. A new feature is the possiblity to change side-chain rotamers. 3207The procedure is now: 3208 32091) load in a PDB file 32102) click the zmatrix button and create a zmatrix for this protein 32113) click the backbone button 32124) NEW click on the backbone with the SECOND mouse button and a popup 3213 window with side-chain commands will appear: 3214B 3215 3216 switch on display of this amino-acid, replace amino acid, replace rotamer 3217 32185) Switch to full zmatrix to edit individual atoms 32196) click in the zmatrix on the Chi1-4 edit boxes with the second mouse 3220 button and select "animate", click the edit box again to end the animation. 3221 32227) click in the Molden Control window the button "Hetatm" and switch on 3223 Helix, Beta sheet, and coil and optionally any hetatm records. 32248) click on the Vr icon (7th from the top) and select OpenGL 3225 (you need to have the molden opengl helper program installed for this, 3226 moldenogl) to get a high quality opengl display of your protein. 3227 3228The z-matrix is only used for manipulation of the protein, a zmtrix of a 3229protein should never be saved, instead the updated result should be stored in 3230PDB file. 3231The disadvantage of this new approach is a much more complicated algorithm, 3232in which undoubtable some bugs have found there way home. 3233 3234 3235------------------------------------------------------------------------ 3236 Molden4.1 3237 3238Wed Jul 21 3239 - The zmatrix conversion for proteins containing nucleotides 3240 has been improved, it will now create a zmatrix. 3241 Still No manipulation of nucleotides however. 3242 3243 3244 - The windows version of molden now start the opengl 3245 helper program mogl, when you click a *.ogl file 3246 in the read file window. 3247 3248Thu Jul 15 3249 - Now when you apply the tinker amber force, automatically 3250 the charges associated with the atoms belonging to 3251 amino acid residues are set. 3252 3253 - A user reported that within gaussian03 you can have the 3254 condition that you use pure D functions (5D), but 3255 use cartesian F functions (10F). Molden did not handle 3256 this correctly, it would assume the use of all pure 3257 functions (5D and 7F) or all cartesian (6D and 10F). 3258 Molden can now handle this mixed use of pure and cartesian 3259 D and F functions. 3260 This also has ramifications for the molden file format: 3261 3262 Previously the default was 6D en 10F, the use of the keyword 3263 [5D] would mean 5D en 7F. The new format uses: 3264 3265 - default is 6D and 10F 3266 - [5D7F] means 5D and 7F 3267 - [5D10F] means 5D and 10F 3268 - [7F] means 6D and 7F 3269 3270 for backwards compatibility, [5D] still means 5D and 7F. 3271 3272 - Fixed a bug that would molden not read the Pseudo 3273 Potential information of a G03 run (older versions 3274 were ok). 3275 3276 - Added the [PSEUDO] section to the molden format: 3277 3278 [PSEUDO] 3279 Fe 1 16 3280 .... 3281 3282 This is elementname followed by the number of the atom 3283 and the effective core charge. 3284 3285Wed Jun 16 3286 - fixed bug that would let the windows version of molden 3287 crash when you go to the density mode without having 3288 read in a file (for the benefit of reading gaussian 3289 cube files) 3290 3291 - Molden now checks whether the contraction coefficient 3292 it reads in via gaussian output files and molden format 3293 files contain the normalisation of the contracted 3294 gaussian. 3295 3296 - increased the maximum number of atoms in the density 3297 mode from 300 to 2000, this to the benefit of oniom 3298 calculations. (this is independend of the max number of 3299 basis functions in molden). 3300 3301Wed Jun 9 3302 - Added interactive docking: 3303 3304 - start molden with a PDB/mol2 file containing the pocket 3305 - Click the icon with the two phenyl rings overlayed: 3306 (In the Molden Control window, the nineth icon from the 3307 top). Choose 'Interactive docking' 3308 - Supply the name of the PDB file containing the ligand. 3309 - Follow on screen instructions for rotation/translation 3310 - the Docking Score window will appear, when you rotate/ 3311 translate the ligand, the PMF score will be updated 3312 in this window. 3313 - the window also allows you to store and write combinations 3314 of rotation/translation of the ligand (pose). 3315 The filename pose.xx will be used for written poses. 3316 - The AtomInf button lets you display info on the PMF score 3317 contributions of a picked ligand atom: click on one of 3318 the ligand atoms. The PMF score window will pop-up with 3319 a list of the top negative (=favorable) and top positive 3320 atom-pair contribution for the slected ligand atom. 3321 When clicking on a list entry the corresponding protein 3322 atom of the ligand atom - protein atom pair lights of 3323 on the screen (clicking again will switch it off). 3324 - activating the 'ligand color mode', will color ligand 3325 atoms according to the amount the contribute to the total 3326 PMF score for the ligand. 3327 3328Thu Mar 25 3329 - In the z-matrix editor, you can now use the second mouse 3330 button to select in molecule drawing screen an atom. 3331 Now a change fragment popup box will appear to facilitate 3332 structure manipulation. 3333 3334 - added the ability to read the high level layer orbitals/ 3335 basis-set of an oniom calculation. Apparently the orbitals 3336 are only printed at the first point, NOT at the stationary 3337 point of an optimise run. 3338 3339 - improved the interface to run amber within gaussian. 3340 Parameters are automatically assigned (for amino acid atoms!) 3341 3342 - When using ONIOM with High and Low layers, the charge & 3343 multiplicity check went wrong, fixed it. 3344 3345 3346 PLEASE LET ME KNOW if you use the oniom interface in molden 3347 and have suggestions for inprovement. 3348 3349------------------------------------------------------------------------ 3350 3351 Molden4.0 3352 3353Wed Mar 17 3354 - When there is an error reading the vectors (orbitals) 3355 in gaussian, molden would automatically skip the reading 3356 of ESP charges from gaussian. Fixed this. 3357 - The print format for ESP charges has changed going from 3358 g98 to g03. The new format is now supported. 3359` 3360Mon Mar 15 3361 Fixed a bug that lets molden think that any file that 3362 begins with an empty line is a mopac .gpt file. 3363 3364Mon Mar 1 3365 - Molden didnt correctly parse Gaussian oniom output: 3366 corrected it. 3367 3368 - Added better support for the MacOS system, by adding 3369 an entry to the makefile for the moldenogl program 3370 and adding #ifdef statements to the corresponding 3371 C code, ogmol.c and silly.c 3372 3373Tue Feb 17 3374 - Fixed the reading of gaussian outputfiles when using 3375 the amber forcefield. 3376 3377Fri Feb 13 3378 - Fixed small bug that wouldnt let you display beta 3379 orbitals with the molden commandfile. 3380Thu Feb 5 3381 - Changed common block /freq/ in such a way that 3382 compilers no longer complain 3383 3384Mon Jan 19 3385 - Fixed a problem with the new Multi molden_format, 3386 In case of multiple molecules with vibrational 3387 information, this information was not updated. 3388 3389 - The name of the file read via the filemananger 3390 will now be displayed as the name of the main 3391 graphics window. Same holds for named [MOLECULE] 3392 sections of a multi molden_format file. 3393 3394 - Changed the code of wrzmat.f, this gave problems 3395 on some platforms (AIX). 3396 3397Wed Jan 14 3398 - Fixed a bug that presented it self with g98,g03 3399 xyz optimisation of a molecule with more than 50 3400 atoms. When clicking in the geometry optisation window 3401 on a point, the shown geometry would be out of sync 3402 with the next/movie button geometries. 3403 3404Mon Jan 12 3405 - Fixed a bug that made molden crash every once in 3406 a while on LINUX !!! 3407 3408 - Reduced the flickering of windows when 3409 an other window is moved over it for LINUX. 3410 3411Thu Jan 08 3412 - support for gaussian with pseudopotentials: 3413 Now the proper mulliken charges and density are calculated 3414 3415 - In rare cases gaussian reduces the number of MO's, 3416 making it smaller than the number of basis functions. 3417 Molden can now handle this. 3418 3419Wed Jan 07 - fixed bug reading Molden Format files: 3420 when reading two Molden Format files after each other 3421 and the number of occupied orbitals in the first was 3422 bigger, the second file would have the wrong density 3423 matrix due to some old occupation numbers being present. 3424 3425 - Molden allocates memory for the orbitals dynamically 3426 but not so for the basis-set. This could lead to problems 3427 with very large calculations. I increased the storage 3428 for the basis-set with a factor of 4. 3429 3430 - Added new feature to the Molden format: 3431 3432 Molden format files can now be concatenated in to 3433 one file, provided they are separated by the 3434 [MOLECULE] keyword line. In addition each molecule 3435 can have a [TITLE] line, example: 3436 3437 [MOLDEN FORMAT] 3438 [MOLECULE] 3439 [TITLE] 3440 title molecule 1 3441 .... rest as usual 3442 [MOLECULE] 3443 [TITLE] 3444 title molecule 2 3445 .... rest as usual 3446 3447 If Molden reads such a file, a extra button will appear in 3448 the "select point" section of the molden control window. 3449 When pressed, the titles of the molecule sections will 3450 be listed and when selected the appropriate molecule 3451 section will be read. 3452 Each [MOLECULE] section can have all the previously supported 3453 sections/keywords. 3454 34552004 3456 3457Tue Nov 25 3458 - When reordering a Z-matrix nolonger all atoms have to be 3459 clicked. When hitting the escape key molden will try 3460 to figure out the ordering of the remaining atoms. 3461 3462 - Gaussian03 no longer prints just electronic energy 3463 during SCF, but total energy, when using the #P keyword. 3464 Molden wrongly subtracted the nuclear repulsion energy. 3465 Fixed. 3466 3467 - Added a button near the "first, next and movie" buttons. 3468 When clicked this button will open a window in which the 3469 delay time (in milliseconds) between one structure and 3470 the next. This delay time also has effect on the display 3471 of normal vibrations. 3472 3473Mon Nov 17 3474 - Molden now fully supports 5D and 7F orbitals. 3475 Previously, only orbitals and density were supported, 3476 NOT mulliken charges, electrostatic potential and 3477 multipole expansion. 3478 3479Fri Oct 17 3480 3481 - Via the button "read", there is now the option "add" 3482 available as opposed to "replace" which stand for the 3483 original behaviour. "ADD" adds a structure to the 3484 existing structure on the screen. 3485 Currently this option is ONLY supported for the following 3486 file types: pdb, mol2, and xyz 3487 This option is mainly useful for comparing different 3488 conformations (protein) AND offers the ability to 3489 read in a protein and overlay different docked ligands. 3490 3491 - A mayor overhaul of the PDB editing capabilty via the 3492 Z-matrix editor. This will probably need more work, but 3493 is quite an improvement over the existing situation. 3494 3495 - The Z-matrix editor will now try to keep the original 3496 orientation and translation when translating zmat to 3497 cartesians. 3498 3499 - Molden picks up the normal modes symmetry tag for 3500 Gaussian and Mopac output. 3501 3502 - prelimenary support for Tinker4.1. Tinker4.1 has 3503 different names for the amber and charmm parameters files. 3504 Also a few (non residue) atom types have changed, this is 3505 NOT YET supported. 3506 3507 - use of the gaussian keyword hpmodes caused problems 3508 for molden: fixed 3509 3510 3511------------------------------------------------------------------------ 3512 3513 Molden3.9 3514 3515 3516Tue Aug 26 3517 - calculated spectrum now also supported for mopac 3518 3519Mon Aug 25 3520 - corrected bug that didmt read old gaussian freq 3521 outputs 3522 3523Wed Aug 20 3524 - Corrected a bug in the new calculated spectrum part. 3525 This bug only manifested itself when the number of 3526 frequencies exceeded 200. 3527 3528Mon Jun 30 3529 - Corrected Gaussian03 frequency reading 3530 3531 - Now with PDB file writing, the original residue number 3532 is maintained 3533 3534 - You use an expression like *:A to turn on all residues 3535 of the A chain 3536 3537Tue Jun 17 3538 3539 - Added a feature to display an interactive spectrum 3540 3541 - Added to the Molden format an item: 3542 [INT] 3543 intensity1 [raman_intensity1] 3544 intensity2 [raman_intensity2] 3545 ... 3546 intensityn [raman_intensityn] 3547 3548 - Added the support for gamess-us Natural orbitals 3549 3550------------------------------------------------------------------------ 3551 3552 Molden3.8 3553 3554Thu May 22 3555 - Gaussian03 basis-set output has slightly changed 3556 with respect to Gaussian98, this would cause error 3557 in molden with molecules with more than 9 atoms. 3558 Fixed it. 3559 3560Wed May 21 3561 - When forces or displacement were to large, Gaussian 3562 would print ******* 3563 Molden couldnt deal with that, now it can. 3564Tue May 20 3565 - Support for mopac2000 ASCII gpt files 3566Tue Apr 29 3567 - 3Ddrc gamess-us IRC support 3568Wed Apr 16 3569 3570 - First support for Gaussian03 3571 3572Tue Apr 01 3573 3574 - PDB residue numbering is now consistent with those 3575 in the actucal PDB file 3576 - MOPAC grid search output is now somewhat supported 3577 - Drawing errors for coil secundary structure are 3578 reduced 3579 - In the Z-matrix for PDB entries, HETATM's will 3580 be attached to the backbone instead of the closest atom. 3581 3582Mon Feb 17 3583 - Added the ability to write MDL mol files. 3584 - Added the ability to calculate EEM charges, 3585 a sort of gasteiger charges, by Patrick Bultinck 3586 - The reading of PDB files now handles additional 3587 Hydrogen labels 3588 3589Wed Dec 04 3590 The oniom stuff had a bug for the linux version, fixed. 3591 3592Thu Nov 28 3593 Added an update to the ONIOM window. 3594 3595Tue Nov 05 3596 - Complete update of the Gamess-UK dedicated code by 3597 Huub v. Dam: 3598 3599 - Reading of SCF-convergence for CASSCF and DFT 3600 - Reading of CASSCF orbital occupancies 3601 - Support for HESSIAN jobs added 3602 - and more ... 3603Thu Oct 17 3604 - Added support for the CPMD program 3605 Distributed with the permission of TEODORO LAINO 3606 NEST Laboratories - INFM - Scuola Normale Superiore 3607 Some work still needs to be done. 3608 3609Fri Oct 11 3610 - Added makefile entry for Mac OSX, thanks to Eric Brown. 3611 3612Wed Sep 25 3613 3614 - Molden3.8 has support for tinker3.9, older versions of 3615 tinker are not supported (Molden3.7 support tinker3.6) 3616 (Thanks to Nicolas Ferre) 3617 3618 - Nicolas Ferre added support for ONIOM calculations with 3619 gaussian98. 3620 3621 - In submit gaussian window you can specify 3622 you want to write cartesian coordinates instead of z-matrix. 3623 3624 - You can now run amber from gaussian, in the following way 3625 Read in a pdb file, click the z-matrix button and create 3626 a z-matrix, assign tinker amber atom types (the FF button) 3627 Go to submit job option gaussian, choose method "amber" 3628 "Write XYZ" form the "Gaussian Job" window. 3629 In principle this can be combined with the oniom method 3630 but this is not tested yet. 3631 3632 - When introducing Mopac2000 support a bug was introduced 3633 which interfered with the reading of tinker xyz files, fixed. 3634 3635 3636 Molden3.7 3637 3638Wed Sep 25 3639 - When introducing Mopac2000 support a bug was introduced 3640 which interfered with the reading of tinker xyz files, fixed. 3641 3642Mon Jul 08 3643 - Correction added to the postscript plot. 3644 - added F and Cl as hydrogen-bond donors 3645 3646Mon Apr 08 3647 - Gamess-US version 16 FEB 2002, has a slightly different 3648 basis-set section. Molden now supports this. 3649 3650Fri Apr 5 - Added support for reading Mopac2000, out and arc files. 3651 3652Wed Mar 20 3653 - added some small changes to the automatic xyz->z-mat 3654 conversion 3655 3656Wed Mar 13 3657 - when mol2 files would miss residue information 3658 molden would display the structure, fixed 3659 3660 - when reading xyz files containing multiple structures 3661 containing energy values in the title line, energy values 3662 of zero, would not be correctly read on the second time 3663 a multiple xyz structure was read. Fixed this. 3664 3665Tue Mar 05 3666 - The introduction of a extra line "FORCE CONST.:" when 3667 running a force job with gamess-us, caused molden 3668 to not find the normal coordinates. Fixed this. 3669 3670 - When running a Gaussian job using F functions, molden 3671 incorrectly calculated the ESP charges. Fixed this. 3672 3673 - added an option to read the ESP charges calculated by Gaussian 3674 Under the surface icon there is a new option "read ESP charges" 3675 3676 3677YEAR 2002 3678 3679 3680 3681Thu Nov 15 3682 Adapted the script multi_vrml_orbitals.csh to deal with 3683 the changed VRML orbitals. 3684 3685Tue Oct 02 3686 The Gamess-UK orbital occupancy section has changed, 3687 molden now deals with it. 3688 3689Thu Aug 30 3690 3691 - Assigning sybyl force field atom types sometimes failed 3692 to assign aromatic types, fixed it 3693 - Now support for different spacegroup setting in mol2 3694 file (the CRYSIN line, setting field (75-142 alternative 3695 settings are NOT supported)). 3696 - Molden now reads mol files, only 3D tested. The mol file 3697 is recognized when the string V2000 or V3000 is present. 3698 3699Wed Jul 25 3700 The Gamess-UK optxyz output has changed, molden gave errors 3701 with these new outputs, fixed it. 3702 3703Tue Jul 17 3704 - Added a conversion program to convert CADPAC output to 3705 molden format (cad2mol). This program was written by 3706 Mariusz Klobukowski (Mariusz.Klobukowski@ualberta.ca). 3707 This program is now distributed together with the molden 3708 source, to compile it type: 3709 3710 make cad2mol 3711 3712 To run it: 3713 3714 cad2mol 'cadpac_output'.out 3715 3716 A file 'cadpac_output'.mdn will be created, molden will 3717 be able to read it. 3718 3719 3720Mon Jul 09 3721 - Molden did not allow to subsequent subtractions of 2D grids 3722 (gridfile) from the current (density) grid. 3723 Rho_AB - Rho_A - Rho_B was not possible. Corrected for it. 3724 - Molden nolonger recalculates the density before reading / 3725 writing a 2D grid, this make it possible to write 3726 subtracted grids. 3727 3728Fri Jun 29 3729 - Added the possibility to render orbitals transparent 3730 in VRML2.0 by clicking on them 3731 Commandline flag -k adds background + a light. 3732 This is to overcome a very dark scene on some terminals. 3733 3734Thu Jun 21 - added small correction to the reading of 3735 GAMESS-US outputs (when SCFTYP= and RUNTYP=HESSIAN 3736 were not on the same line in the input file, molden 3737 would not display the vibrations). 3738 Thanks to Georgy Salnikov, NMR Group, 3739 Novosibirsk Institute of Organic Chemistry, Russia 3740 3741Thu May 31 - Added support for writing mopac2000 input 3742 containing crystal information (Tv vectors) 3743 3744Tue May 15 3745 - Added support for mopac2000 output containing crystal 3746 information (Tv vectors) 3747 3748Mon May 14 3749 - Removed a bug in reading pdb files containing just 3750 HETATM records. 3751Thu May 10 3752 - REMOVED MAYOR BUG in reading new basis-set section 3753 of GAMESS_US !!!!! 3754 3755Thu May 9 - Molden can now launch a G98W session on windows 3756 3757Thu Apr 19 3758 - Addded new makefile section for HP-UX 3759Mon Apr 2 3760 - The Z-matrix editor option "substitute atom by fragment"-> 3761 "Read" sometimes passed the wrong filename, fixed it. 3762 3763Tue Mar 13 3764 - Molden sometimes crashed on the OPTXYZ output of 3765 Gamess-UK. Fixed thanks to Huub van Dam. 3766 3767Wed Mar 07 3768 - Molden now deals with changed writing o MCSCF orbitals 3769 of Gamess-US. 3770 3771 - Gaussian98 by default only prints the Z-matrix and resultant 3772 coordinates ONLY for 50 atoms or less. However molden 3773 didnt respond correctly when this default was overridden 3774 with the keyword: IOP(2/11=1). Fixed. 3775 3776Tue Dec 19 3777 -Added Option to specify opt=z-matrix in the "submit job" 3778 for Gaussian, available from the Z-matrix editor. 3779 This forces Gaussian to use the Z-matrix when optimising. 3780 The default is to use a nonredundant set of 3781 internal coordinates 3782 3783 - Molden should now nolonger crash on empty files 3784 3785Mon Nov 27 3786 Molden format in combination with both alpha and beta 3787 spin orbitals gave problems when more than 128 orbitals 3788 were present solved it. 3789 3790Tue Oct 31 3791 3792 Added the ability to visualize protein secondary 3793 structure elements such as helices,strands and coil 3794 with the OpenGL helper program. The procedure is 3795 as follows: 3796 3797 - you read in your protein 3798 3799 - you click the "BackBone" button 3800 (If you do not, all of your protein atoms will 3801 visible in the OpenGL, making it extremely slow, 3802 except for small polypeptides) 3803 3804 - you select ligands via the "HetAtm" button 3805 No need to select "Helix","Beta","RNA/DNA" or "coil", 3806 they will automatically be included in the OpenGL. 3807 3808 - select separate residues to be displayed by clicking 3809 "Residue" and then clicking on the backbone on the 3810 screen. 3811 3812 - Decide wether you want the residues and ligands to 3813 be displayed as tubes (default) or as spacefilling 3814 The latter can be switched on by clicking "Solid" 3815 -> "Space Filling" 3816 3817 - Decide wether you want the residues and ligands to 3818 colored by their elements or by residue/ligand color 3819 This is controlled by the "StickColor" button. 3820 3821 - Now click the "Vr" icon and select "OpenGL" 3822 Molden will create a file called "molden.ogl" 3823 and start up the OpenGL helper program "moldenogl" 3824 Remember to rename this file if you want to keep 3825 it, otherwise molden will overwrite it the next time. 3826 3827 - At anytime you can visualize this file again, without 3828 having to start molden by typing: 3829 3830 moldenogl 3831 3832 or: 3833 3834 moldenogl molden.ogl 3835 3836 - use the moldenogl cammand line flag "-r" is you 3837 want to use high quality spheres and cylinders. 3838 This will increase the graphics quality at the expense 3839 of speed of rotation. 3840 3841 - Use the left mouse button to rotate your molecule. 3842 In combination with the "Ctrl" and "Shift" button 3843 respectively, a zoom and translation are performed. 3844 3845 - The third mouse button will bring up menu with 3846 lots of option, of which the "Screen Capture" 3847 option allows you to save your picture as screen 3848 dump postscript or "Vector Postscript". The latter 3849 take longer but will yield a better picture on a 3850 native postscript printer. 3851 3852 - molden has a new commandline option "-z", this 3853 will let molden use more polygons and will 3854 result in a better opengl picture (at the expense of 3855 speed, but ideal for a good postscript picture 3856 in combination with the moldenogl -r flag). 3857 3858 - you can edit the "molden.ogl" file, 3859 specifically the following section is important: 3860 3861 [COL STRANDTOP] 0.0 0.0 1.0 3862 [COL STRANDBOTTOM] 1.0 0.0 1.0 3863 [COL HELIXOUT] 0.0 1.0 0.0 3864 [COL HELIXIN] 0.6 0.6 0.6 3865 [COL RNA] 0.5 1.0 0.5 3866 [COL COIL] 1.0 1.0 1.0 3867 3868 This defines the color of the beta strand (first two), 3869 the helix outer and inner surface (following two), 3870 and the RNA and Coil parts respectively. 3871 3872 They are used further down the file: 3873 3874 [RIBBON] HELIXOUT 3875 3876 Alternatively you may supply a color per ribbon, 3877 by supplying rgb triples (red,green,blue): 3878 3879 [RIBBON] COLOR 1.0 0.0 0.0 3880 3881 3882 In molden you can now also select "coil". 3883 In addition you can click on the helix,strand or 3884 coil to activate a residue (in combination with the 3885 "Residue" button. 3886 3887 Also added the writing of POVRAY files of the ribbon 3888 cartoons as desribed above. Follow the same procedure 3889 to generate then, except that you have to choose 3890 "Povray" under the "Vr" icon. 3891 3892 Molden3.6: 3893 3894Fri Sep 15 3895 - Gamess-us (After Jan10 2000) outputs gave problems 3896 on 64-bit Alpha-linux systems, corrected it. 3897 G77 compiler flag -mieee has to be added. 3898 3899Tue Sep 12 3900 - Added screen capture possibilities to the OpenGL 3901 helper program moldenogl. Three options: 3902 3903 - IRIS RGB format (key F10) 3904 - greyscale encapsulated postscript (key F11) 3905 - PPM bitmap file (key F12) 3906 3907 added a menu option "screen capture" holding the 3908 above three options 3909 3910 Thanks to Pedro Vazquez for supplying the code for 3911 postscript and PPM writing. 3912 3913Mon Aug 21 3914 3915 - Problem with reading shelx files generated by 3916 the CSD's conquest code: 3917 3918 SYMM .5+x, .5+y, z 3919 3920 Molden expected all capitals, fixed to handle 3921 lower case. (All commands must still be in uppercase 3922 however). 3923 3924 - Trying to edit the cell parameters of a structure 3925 read in as shelx file, made the program core dump, fixed. 3926 3927Thu Aug 17 3928 - Added keywords to enable mapping of properties 3929 onto a isosurface with Gaussian Cube files, example: 3930 3931 title 3932 GAUCUB=meto_dens.cube MAPFIL=meto_esp.cube VRML2.0 3933 SPACE=0.001 MAPVAL=(-0.3,-0.1,0.0,0.1,0.3) 3934 3935 GAUCUB for the Gaussian cube containing the density 3936 MAPFIL for the Gaussian cube containing the property 3937 (like the electrostatic potential) 3938 MAPVAL use to change the default property values 3939 associated with the 5 basic colors used 3940 for interpolation 3941 (default values: (-0.1,-0.05,0.0,0.05,0.1)) 3942 3943 3944 Remember currently mapping only works with VRML2.0 3945 and OpenGL output. 3946 3947 - Added a program called 'short_wrl' written by 3948 Andreas Klamt of COSMOlogic, to remove redundant 3949 vertices from moldens VRML2.0 files 3950 To build it type: make short_wrl 3951 To run it: short_wrl molden.wrl 3952 Now molden.+.wrl contains the new VRML2.0 file 3953 3954Fri Aug 11 3955 - The GAMESS-US basis-set output section has changed 3956 molden has been updated to deal with this 3957 3958 - Molden now also writes a '[LINES]' section to 3959 the molden.ogl file. This is the input file for the 3960 molden OpenGL helper application moldenogl. 3961 Older versions of moldenogl may have problems with 3962 this new section. 3963 The [LINES] section has been constructed to visualize 3964 the cell and alpha helices and beta strands. 3965 3966 - Added a few options to the moldenogl, when clicking 3967 with the third mouse button in the main drawing window 3968 you find a menu with as new option 'Animation' 3969 this options under it will allow you to stop/start the 3970 animation, advance by one point (also key 'n' or 'N') 3971 and lets you slow down animations. 3972 3973Fri Jun 30 3974 3975 - GAMESS-US has a changed writing when using pure 5D 3976 molden now deals with in (Thanks to Fred Arnold) 3977 3978 - the moldenogl helper program can now also be called 3979 from the 'molecular mode', it will do normal vibration 3980 animations and animations of molecular reactions. 3981 (Via the VR icon->Opengl). 3982 the molden.ogl format now accepts more molecules. 3983 Added the option -l,-p,-b number to moldenolg 3984 3985 -l = low resolution molecule (faster) 3986 -p = perspective mode on 3987 -b number = choose background color 3988 3989 Added also to the popup menu, including a fullscreen 3990 option, and a light2. (three lights 0,1,2) 3991 3992Mon Jun 26 3993 3994 - The routine reading XYZ files had a problem reading 3995 actinium 'ac', fixed it 3996 3997 - Added a number of things to the opengl helper program 3998 moldenogl, accesible via the menu (third mouse button click): 3999 4000 + transparency toggle (or 't') 4001 + switching on/off of lights 1 through 3 (or '1','2','3') 4002 + fullscreen option (or 'f') 4003 + perspective mode (or 'p') 4004 4005 4006Thu Jun 15 4007 4008 - Added the possibility to create an isodensity surface 4009 colorcoded with the electrostatic potential. 4010 Needed are two gaussian cube files or two molden 4011 3dgridfile's (you can create these by clicking 4012 'write grid' after a 'space' calculation. 4013 Molden will always create a file called '3dgridfile') 4014 Currently only "Opengl" and VRML2.0 output is supported 4015 You will need the updated version of 'moldenogl' 4016 to view the OpenGL output. 4017 For an explanation how to to this see URL: 4018 4019 http://www.cmbi.kun.nl/~schaft/molden/mapped.html 4020 4021 For an example VRML2.0 file: 4022 4023 http://www.cmbi.kun.nl/~schaft/molden/wrl/gamuk.wrl 4024 4025 Added to 'moldenogl' opengl helper is a menuitem 4026 (Third mouse button click) 'transparency' 4027 In the molden file select window, a click on a file 4028 ending with the name '.ogl' will bring up moldenogl 4029 with this file. 4030 4031Fri Jun 09 4032 - When a job required more than the default 256 4033 orbitals, molden allocated more memory, but as a result 4034 the HOMO and LUMO buttons of the xwindows interface 4035 nolonger worked correctly. Fixed it. 4036 4037Mon Jun 5 4038 - Jeffrey Frey and James Hess have suggested a small 4039 adjustment of the [MOLDENOGL] format. 4040 You can now adjust the transparency of a surface by adding 4041 a number: 4042 4043 [SURF] TRANS 0.75 4044 4045Wed May 31 4046 4047 - When reading molden format files with more than 256 4048 orbitals, some arrays were overwritten, fixed it. 4049 4050 - In z-matrix editor: the check box to specify 4051 Gamess-US style z-matrix writing now print a 4052 small explaining message when operated 4053 4054Fri May 12 4055 - Molden generated Povray orbitals had swapped 4056 colors with respect to VRML and OpenGL orbitals 4057 This is corrected. 4058 (blue = positive, red= negative) 4059 4060 4061Thu Apr 27 4062 4063 - BIOSYM/MSI car files for non-periodic work again 4064 4065 - In z-matrix editor: instead of "clear status all variables" 4066 you now get the option to set the status to variable 4067 or constant 4068 4069 - In z-matrix editor: Added a check box the specify 4070 Gamess-US style z-matrix writing 4071 4072 - In z-matrix editor: when typing "c" in the main drawing 4073 window molden will look for a file "mapfile" which 4074 contains coordinates to orient cartesian coordinates 4075 after z-matrix -> cartesian conversion 4076 Example "mapfile" 4077 4078 1 50.006 81.343 67.412 4079 2 50.599 80.892 66.194 4080 3 49.514 80.759 65.162 4081 4082 Contains coordinates (angstrom) of atoms numbered 1,2,3 4083 4084Thu Mar 30 4085 4086 - Molden now nolonger always creates the file 'plot' 4087 The xwindow interfaces doesnt, here you generate 4088 a postscript plotfile by clicking the corresponding button. 4089 Only when supply you molden with a keyword file it will 4090 create the plot file 4091 4092Thu Mar 23 4093 - Added primitive support for Jaguar cube files 4094 No molecular geometry is displayed however. 4095 Start molden without a filename on the commandline 4096 Go to the density mode, click "Read Cube", chose "Jaguar" 4097 supply a filename, then click the "space" button and supply 4098 a contour value. 4099 4100Tue Mar 14 4101 4102 - Fred Arnold added support for reading Gamess-us 4103 orbital localisation schemes; Pipek-Mezey and 4104 Edmiston-Ruedenberg 4105 4106Thu Mar 09 4107 4108 - Changed povray writing didnt work for orbitals, 4109 corrected by Fred Arnold 4110 4111Wed Mar 08 4112 4113 - Under edit cell parameters, you can now also specify 4114 a spacegroup name, instead of just a spacegroup number. 4115 4116Fri Mar 03 4117 4118 - support for Gamess-us version with long contraction 4119 coefficients. 4120 4121Tue Feb 29 4122 - Fred Arnold updated the writing of povray files. 4123 4124Thu Feb 24 4125 4126 - Molden now nolonger dies when you kill one of its windows 4127 4128 - Added a restore color options, under the color palette 4129 icon 4130 4131Wed Feb 23 4132 - molden used to center a molecule by working 4133 on the atomic coordinates directly. 4134 Now this is accomplished via a viewing transformation 4135 the coordinates are not affected. 4136 4137 - In principle now the conversion of a z-matrix to 4138 cartesian takes into account the original orientation 4139 of the molecule in cartesian space 4140 4141Fri Feb 11 4142 - Added writing of CML molecules (primitive) 4143 4144 - With the introduction the new style of rotation 4145 there was a clash between the use of control 4146 for zooming in and for temporarily escaping selecting 4147 of atoms, under the "Reorder Z-matrix" button of the 4148 Z-matrix editor 4149 4150Wed Feb 02 4151 4152 - Added dynamic memory allocation for reading mopac .gpt 4153 files. 4154 4155 - corrected reading of *.ogl files by moldenogl, 4156 created with mopac .gpt files. 4157 4158Mon Jan 31 4159 - added commandlineflag to adjust the maximum number 4160 of Gif files molden will write (default 100) 4161 molden -j 2000 4162 Molden will write 2000 files at the max. 4163 4164Fri Jan 28 4165 - While adding OpenGL support some errors were 4166 introduced for the platforms VMS, CRAY and AIX 4167 4168Mon Jan 24 4169 4170 - Full support to view orbitals/density etc. in OpenGL 4171 This is accomplished via a helper program called 4172 'moldenogl', this needs to be build separately. 4173 (make moldenogl), you need to place this program 4174 in a directory which is in the default path, say 4175 /usr/local/bin. You can evoke it from the Xwindows 4176 interface under the 'Vr' icon, option OpenGL. 4177 Molden will write a file 'molden.ogl', which will 4178 be read by the helper program. If you want to save 4179 this file you will have to rename it before you 4180 choose OpenGL again. You can run 'moldenogl' standalone. 4181 4182 moldenogl file.ogl 4183 4184 This has been tested for Silicon Graphics and linux. 4185 The latter needs the MESA graphical library 4186 have a look at URL: http://www.mesa3d.org/ 4187 You may need to activate the 'LIBSG' line for your 4188 platform. 4189 4190 HOW TO OPERATE MOLDENOGL: 4191 4192 Use the mouse to rotate the scene, drag while holding 4193 down the left mouse button. 4194 Further one letter commands: 4195 4196 Left Mouse button - rotate 4197 Left Mouse button + Shift - translate 4198 Left Mouse button + Control - zoom in / out 4199 Right Mouse button - bring up options 4200 4201 m - toggle molecule 4202 x,y,z,X,Y,Z - move position of light 4203 4204 4205 PS. On linux the mesa libraries are installed in the 4206 the directory /usr/local/lib. This may give the 4207 problem that moldenogl cant find these libraries, 4208 you can remedie this by either copying the libraries 4209 to /usr/lib, or setting the environment variable; 4210 LD_LIBRARY_PATH, in say /etc/csh.cshrc 4211 (setenv LD_LIBRARY_PATH "/usr/lib;/usr/local/lib") 4212 4213 4214 You generate .ogl file from a molden keyword file by use 4215 of the keyword OPENGL. 4216 4217 - added comandline option -t, which will let molden read 4218 chem3d style ascii .gpt files (mopac93) 4219 4220 - added a threshhold for plotting displacement vectors 4221 in the postscript output of a normal mode. 4222 You can set it via the -y commandline flag: 4223 4224 molden -y 2.0 4225 4226 (default the threshhold is 0.0, every arrow is plotted) 4227 4228 Thanks to: 4229 4230 Valentin P. Ananikov 4231 NMR Group 4232 ND Zelinsky Institute of Organic Chemistry 4233 Moscow, Russia 4234 e-mail: val@cacr.ioc.ac.ru 4235 4236 (URL: http://nmr.ioc.ac.ru/Staff/AnanikovVP/molden-t/ 4237 PS: the path uses the -t commandline flag, this is now -y) 4238 4239 4240Thu Jan 13 4241 4242 - The color editor didnt work well on linux, fixed it. 4243 4244Wed Jan 12 4245 - Added first primitive support for OpenGL, 4246 4247 THE BELOW IS OUTDATED HAVE A LOOK AT THE ENTRY FOR Jan 24 4248 4249 read the makefile on how to activate it. 4250 It only works for Silicon Graphics machines and 4251 linux machines. The latter needs the MESA graphical 4252 library. Currently only a the equivalent of the 3dx mode 4253 is available. 4254 You can only activate the OpenGL via a molden keyword file, 4255 and the use of the keyword 'silly', file 'molin' 4256 4257 Title 4258 file=test/adf.molf silly homo 4259 4260 ./molden molin 4261 4262 Use the mouse to rotate the scene, drag while holding 4263 down the left mouse button. 4264 Further one letter commands: 4265 4266 m toggle molecule 4267 . zoom in 4268 , zoom out 4269 x,y,z,X,Y,Z move position of light 4270 4271 - Added the another type of molecular rotation model. 4272 It is available via a new icon in the lower right 4273 corner of the 'Molden Control Window'. 4274 In this model you rotate the molecule by dragging 4275 the mouse while holding down the left mouse button. 4276 Doing the same while keeping the 'Shift' button pressed 4277 lets you translate the molecule. 4278 Doing the same while keeping the 'Control' button pressed 4279 lets you zoom in/out. 4280 4281Wed Jan 05 4282 4283 - Added maxmimum line width selection under: 4284 the palette icon, the option: 'shade depth'. 4285 4286Wed Dec 22 4287 4288 - Added depth of shade editor, under the palette icon 4289 there is a new option: 'shade depth'. 4290 This option has no effect on the solid drawing mode 4291 with perspective off, only the stick mode and 4292 solid+perspective modes are affected. 4293 4294Tue Dec 21 4295 4296 - Added the ability to edit colors, under the palette icon 4297 there is a new option: 'edit colors'. This option will 4298 edit the basic 15 colors available in molden. It will 4299 write the colors toe the file '.moldenrc' in the users 4300 home directory. The use of 'molden -r colorfile' takes 4301 precendence over the reading of .moldenrc. 4302 To reset to the defaults just remove the ~/.moldenrc file 4303 4304Thu Dec 9 4305 4306 - the WRZMAT keyword now writes the last z-matrix of 4307 say a geometry optimisation, instead of the first 4308 4309 - added the commandline flag '-=', which causes a 4310 gamess-us dialect of gaussian zmatrix to be written, 4311 it has the = sign between variable names and values 4312 For use with COORD=ZMAT 4313 4314 - Gamess-UK6.2 energies of the geometry convergence 4315 were not read properly, fixed it 4316 4317Wed Dec 08 - Updated the makefile entry for CRAY unicos, for 4318 running the f90 compiler 4319 4320Thu Dec 02 4321 - writing of non-periodic MSI files used atomic units 4322 rather than angstroms, corrected it. 4323 4324 - When writing postscript in the molecular mode, molden 4325 will check for dummy atoms and will ask you if you 4326 want to include them in the plot. In the current situation 4327 dummies where not plotted. 4328 4329 - In the molecular mode you can change the connectivity 4330 of the atoms, but not so in the density mode. This proved 4331 a problem for people generating VRML orbitals of metal 4332 complexes, i have solved this ONLY for the VRML writing: 4333 4334 Before it will write the VRML molecule, it will check 4335 for the existence of a file called 'molden_connect' 4336 (be sure you have the permission to read it, 4337 ls -l molden_connect), this file should hold the 4338 connectivity of the molecule, per line two number; 4339 atom1 atom2 If atom2 is negative, molden will read an 4340 extra line with 5 numbers it will average the 4341 coordinates of these 5 atoms and create a bond 4342 between atom1 (of the first line) and the average over 4343 the 5 atoms (of line two), it will use the color 4344 associated with the first atom of line two. If you want 4345 to average over less then 5 atoms just supply 4346 zeros for the remaining atoms 4347 (so avg over 3: i1 i2 i3 0 0) 4348 4349 DONT FORGET TO REMOVE OR RENAME THE 'molden_connect' FILE 4350 AFTERWARDS. 4351 4352 - When you select atoms in the Z_matrix to 'cut out' a part 4353 of the atoms to create a new z-matrix, properties like 4354 atoms types, forcefield types, color, residue and charge 4355 are now inherited. 4356 4357Thu Nov 18 4358 - Added keyword POVRAY, to generate the povray file molden.pov 4359 - Added support for Ampac style cube files 4360 4361Thu Nov 11 - Fetched some minor problems: 4362 4363 - some msi files were not read correctly, fixed 4364 - gamess-US, sometimes doesnt end coordinates 4365 with an empty line, but with: 4366 '...... END OF ONE-ELECTRON INTEGRALS ......' 4367 dealt with 4368 - the geometry convergence window sometimes didnt 4369 update correctly, fixed it + made them smaller (for PC) 4370 - when moving atoms in a cell you couldt use the 4371 distance button anymore, fixed it 4372 4373Tue Oct 12 - Solved problem when replacing last amino acid 4374 4375Thu Oct 7 - Reading msi files generated stray atoms when H-bonds 4376 where present in the msi file, resolved. 4377 4378Thu Sep 30 4379 4380 - First support for GamessUK6.2, now coping with changed 4381 orbital writeout 4382 4383 - Added Button to the Z-matrix window to make it smaller. 4384 4385 - GLX and ASX PDB residues are mapped to GLN and ASN 4386 GLX and ASX caused problems in protein z-matrices 4387 4388Mon Sep 20 4389 4390 - fixed bug: when creating a peptide via the z-matrix 4391 closing the z-matrix window and then opening it again 4392 caused molden to crash. 4393 4394 - Added support for MOL2 protein files, small molecules 4395 were already supported. 4396 4397 - Added support for reading/writing MSI Cerius files, 4398 The reading is NOT robust, it will read simple, periodic 4399 structures 4400 4401Thu Sep 9 4402 4403 Molden now uses dynamic memory allocation for the 4404 size of the grid, this will allow you to read in 4405 any size gaussian or vasp cube files. 4406 It also allows you to redefine the size of the grid 4407 in points from the 'plotplane' window, via the commnds 4408 nptsx= nptsy= nptsz= 4409 Previously the maximum was nptsx=nptsy=nptsz=61 4410 4411 The molden version created with 'make noxwin' is NOT 4412 dynamic. 4413Mon Sep 6 4414 4415 Molden now uses dynamic memory allocation in some 4416 parts of the program: 4417 4418 - For a z-matrix of a protein 4419 (Not for reading a z-matrix of a protein) 4420 4421 - For basis-sets larger than 256 orbitals 4422 4423 Not done are for instance the maximum size of a grid 4424 (which is 61*61*61), so cube files with larger dimensions 4425 are still a problem 4426 4427 The molden version created with 'make noxwin' is NOT 4428 dynamic. 4429 4430Mon Aug 23 4431 4432 Linked Z-mat variables were not updated onscreen. 4433 Non bonded atoms in the stick mode were not correctly 4434 shown in the postscript output 4435 4436Thu Aug 19 4437 4438 A word of WARNING: 4439 4440 Molden3.6 has gone through quite a few 4441 drastic changes, it can therefore be expected to have a few 4442 bugs introduced, so for the time being use this version 4443 at your own risk, and PLEASE report any problems you 4444 encounter (schaft@caos.kun.nl) 4445 4446 - Improved filemanager, it now also works correctly in 4447 directories other that the current. 4448 A directory select window has been added. 4449 4450 - More labels options: added "pdbsymbol","residue" 4451 4452 - Molden now treats any color depth greater or equal 8 4453 as having 256 color cells 4454 4455 - Molden "Author" icon has been replaced by the "FF" icon 4456 which when clicked pops up the ForceField type assign 4457 window. You can still invoke the author window by typing 4458 "a" in the drawing window. 4459 4460 - Typing "u" in the drawing window, brings molden secondary 4461 windows ontop of the drawing window. (This may not work 4462 with the gnome window manager). 4463 4464 - In the stick drawing mode, atoms which are not bonded 4465 used to be invisible, they are now represented as crosses. 4466 4467 - When saving a structure as PDB file it will ask you 4468 if you want to write the Hydrogens or not. 4469 4470 - Under the "H" icon an option has been added to 4471 recalculate the H-bonds. 4472 4473 - The biggest addon is the pdb to z-matrix conversion, 4474 in essence this was already there in the 3.5 version, 4475 but was very buggy (there will probably be some more :-)) 4476 In the 3.5 version the whole z-matrix of the protein was 4477 shown, which is way to much and cumbersome to handle. 4478 In 3.6 the default is to create a z-matrix representation 4479 which list the aminoacids with its phi,psi and chi angles. 4480 You can click on the Aminoacid button and choose from a 4481 number of options: 4482 4483 Switch On 4484 Switch Off 4485 Center 4486 Contacts 4487 Delete 4488 Insert 4489 Replace 4490 4491 The one letter codes are also displayed. You can search 4492 with a string of one letter codes. There is a button to 4493 go to the "full Z-matrix" 4494 4495 Unlike the old behaviour, ONLY variables which were changed 4496 on screen are updated in the internally stored z-matrix 4497 4498 IMPORTANT: 4499 4500 MOLDEN WILL ONLY PROMPT YOU TO CREATE A Z-MATRIX 4501 FOR A PDB FILE WHEN IT HAS ENOUGH ROOM TO STORE 4502 THE Z-MATRIX, DEFAULT IT WILL ACCOMODATE 1000 ATOMS, 4503 NOT ENOUGH FOR MOST PROTEINS. SO YOU HAVE TO CREATE 4504 A BIGGER VERSION OF MOLDEN: 4505 4506 - edit the file "change_parameter" 4507 - replace the body: 4508 4509 1,\$s/maxorb=256/maxorb=1024/ 4510 1,\$s/numatm=150/numatm=300/ 4511 4512 by: 4513 4514 1,\$s/maxat=1000/maxat=20000/ 4515 4516 - save this file and execute it: 4517 4518 ./change_parameter 4519 4520 4521 - change_parameter only works on the fortran files 4522 you have to edit the C code manually: 4523 4524 - edit xwin.c, replace: 4525 4526 #define MAXAT 1000 4527 4528 by: 4529 4530 #define MAXAT 20000 4531 4532 - save the file, and type 'make' 4533 4534 4535 4536 4537 4538 Molden3.5: 4539 4540Mon Jul 19 4541 4542 - Fixed bug which let you not save charges you edited, 4543 when you start of with a file which has no charges 4544 4545Thu Jun 17 4546 4547 - removed small bug in rdgaus.f which made some compilers 4548 stop. 4549 4550 - added the capability to write and read files with custom 4551 spherical atom densities to be used in difference density 4552 plots (bonds keyword). 4553 4554 molden inputfile 4555 4556 inputfile: 4557 4558 some title 4559 file=gaussian_atomic.log genat 4560 4561 a file 'basiinf.mbi' will be written, these can be 4562 concatenated and read back in to molden, fi: 4563 4564 molden -x atomicdens 4565 4566 Thanks to Bjoern Pedersen who implemented it. 4567 (Bjoern Pedersen, Technische Universitaet Muenchen 4568 Institut fuer organische und Biochemie, 4569 Bjoern.Pedersen@ch.tum.de) 4570 4571 4572Thu Jun 3 4573 4574 - Added resizebility of the geometry convergence window 4575 4576 - Removed SERIOUS BUG introduced Fri May 21 4577 4578 4579Wed Jun 2 Added commandline opiton -m, which turns off bell sounds 4580 4581Fri May 21 Added scale factor for normal mode displacement vectors 4582 in the frequencey window. 4583 4584Fri May 7 4585 GAUSSIAN: 4586 4587 - COMPOUND jobs, (optimisation, followed by a FREQ job) 4588 should now be oke. 4589 4590 - Gaussian98 doesnt print 'input orientation', for a 4591 molecule with more than 50 atoms, in this case molden 4592 couldnt show intermediate structures of an optimisation 4593 run, FIXED. (The problem could be fixed by supplying 4594 IOP(2/11=1) but molden now always takes the 'standard 4595 orientation' and disregards forces (for more than 50 atoms)) 4596 4597Tue Apr 27 4598 - Support for reading Gaussian cube files via the 4599 molden keyword file (new keyword GAUCUB): 4600 4601 tlite 4602 gaucub=test/test_homo.cube space=0.1 vrml 4603 4604Thu Apr 22 4605 - Molden can write VASP POSCAR files, under the 'cell' icon, 4606 'write' -> 'write VASP', Molden can also read these files 4607 (Use always 'direct or selective' keywords fullout) 4608 (Use the first line not as title but put the element 4609 names in there). 4610 Read support is rudimentary; POSCAR files have all atoms 4611 lying in the cell, which may give a scattered outlook 4612 of the molecule in the cell. 4613 Molden can also read the VASP density grid files, although 4614 they tend to be too big for the default molden version. 4615 Presently only grids which axes are under 90 degrees 4616 will be accepted. 4617 4618 - Changed under the 'Cell' icon: the seperate write options; 4619 'write DMAREL', 'write SHELX', 'write CRYSTAL95', into 4620 one options 'write', which lets you select out these 4621 options + 'write VASP' 4622Thu Apr 15 4623 - Molden can now generate Gif's for 24-bits displays 4624 4625Fri Mar 26 4626 - Added Possibility to delete and move atoms in a 4627 crystal, under the CELL icon, the last two options. 4628 It was already possible to translate the atoms in a cell 4629 but this was interactively, the new translate option 4630 allows discrete translations (say 0.5 0 0) of selected 4631 atoms in the assymetric unit. 4632 4633Fri Mar 5 4634 4635 - Added commandline flag "-geom XXXxYYY-xxx-yyy" 4636 where XXX and YYY are the size of the window in pixels, 4637 and xxx and yyy are the position of the window in pixels. 4638 4639Thu Mar 4 4640 4641 - Molden can now read Gaussian Cube files: 4642 4643 restrictions: 4644 4645 - these must be formatted cube files 4646 - supported are: density, potential and orbital cubes 4647 (orbital cubes only with ONE orbital!) 4648 - the grid MUST be rectangular 4649 - grid can only be read in the 'density mode' 4650 4651 - Molden now also supports grids which dont have an 4652 equal number of points in all three directions, 4653 and also the radius in the three directions can be 4654 different, under the 'PlotPlane' window there are now 4655 6 new keywords available: 4656 4657 npts1,npts2,npts3 and edx,edy,edz 4658 4659 4660 4661 4662 Molden3.4: 4663 4664Fri Feb 12 4665 4666 - Added support for G98 optxyz output 4667 4668 - Added support for Pluton SPF format 4669 4670 - Added some aminoacid sequence editing stuff 4671 4672Tue Jan 19 4673 4674 - Tinker optimisation of structures in molden is done 4675 in the Z-matrix ordering of atoms, even if the read in 4676 structure is a Tinker xyz file. The last case was not 4677 handled properly, it is fixed. You can optimise in the 4678 original ordering by suppressing the generation of a 4679 Z-matrix by using the commandlineflag -a 4680 4681Tue Jan 12 4682 4683 - Fixed bug in writing chemx .cssr files 4684 - Fixed bug in creating the super cell 4685 - Fixed bug in interpreting molden-format when [5D] 4686 was used. 4687 - Added calculation of electrostatic energy, a new 4688 button 'E q' was added and a field for specifying 4689 the residue number (Eq also calculated interresidue 4690 electrostatics), both in the 'Atom Attributes Window' 4691 this is popped up when you click with the middle 4692 mouse button on a atom. 4693 Shift Mouse click in the residue field lets you set 4694 this residue number to all the atoms you will subsequently 4695 select. 4696 - Added -R npts commandline flag this allows you to 4697 downsize the size of the grid in points. 4698 You can compile with a bigger number of maximum points 4699 (Use the script 'change_parameter': 4700 1,\$s/mx3d=61/mx3d=200/ 4701 to change the grid size, memory is a consideration 4702 since an array of the size mx3d*mx3d*mx3d will be used.) 4703 4704 Thanks to: 4705 4706 Bjoern Pedersen 4707 Technische Universitaet Muenchen 4708 4709 4710Tue Dec 1 4711 - Molden treated Gaussian semi-emirical optimisations 4712 as single points, fixed it 4713 4714 - With Tinker xyz (charmm,amber), the caps are nolonger 4715 (faultily) assigned as residues 4716 4717Mon Nov 30 4718 - Fixed bug that makes molden crash on WinNT/95 and linux 4719 when a mopac GRAPH file is read and the orbital select 4720 window is activated 4721 4722Mon Nov 9 4723 - For the submit gaussian job, molden now also looks 4724 for the g98root environment variable. 4725Tue Oct 20 4726 - support for cssr.arc files. 4727 4728Tue Oct 13 4729 - Removed bug introduced Sep 23, which disabled the 4730 mapping of files onto the z-matrix 4731 - Further integration of wijnand Mooy's xtinker. 4732 4733Mon Oct 5 4734 4735 - Removed a bug which would in some cases now 4736 show a structure in the "molecular mode" for 4737 Guassian98 files. 4738 4739 - Implemented tinker "amber" force field 4740Tue Sep 29 4741 4742 - Removed bug that occured when viewing MO's from MOPAC/VAMP 4743 in the "Molecular Mode" created in the "Density Mode"; 4744 the connectivity of the atoms would be messed up. 4745 4746Mon Sep 28 4747 - Implemented tinker preferences window. 4748 4749Wed Sep 23 4750 4751 - Implemented, real time structure optimising with 4752 tinker mm3 (small molecule) or tinker charmm (proteins). 4753 the molecular display is updated with the intermediate 4754 structures. At the end a tinker archive file is created. 4755 4756 - Support for tinker archive files. 4757 4758 - Vrml from the elctrostatic potential derived from charges 4759 in the density mode, now shows both positive and negative 4760 lobes. 4761 4762 - Adding of fragments can now be done at the start of a 4763 new z-matrix 4764 4765Fri Sep 18 - In submit job (Gaussian, Gamess) the check for charge 4766 and multiplicity gave an error when there was an dummy (X) 4767 present. 4768 4769Mon Sep 7 - Added VRML equivalent of the 3D-X plotting mode, 4770 first select this mode from the Molden Control Window, 4771 then click the "Vr" icon. 4772 4773 - Added creation of peptides. 4774 Click "ZMAT Editor", select "Substitute atom by Fragment", 4775 select "Sequence" and the "Build Sequence Window" will 4776 pop up. Select what kind of conformation you want; alfa 4777 helix, or beta (sheet) alternatively a turn. This selects 4778 the PHI and PSI angles used. You can still change them 4779 in the corresponding PSI and PHI fields. Now specify an 4780 amino acid sequence by clicking on the residue buttons, 4781 a status bar shows the last 16 residues selected. 4782 You can correct an error with the "Undo" button. 4783 When ready click "Build". 4784 Alternatively you can read in a protein file, which should 4785 contain per line: 4786 4787 '3 letter amino acid code' Phi Psi [Omega] [Chi1] [Chi2] 4788 [Chi3] [Chi4] 4789 4790 Everything between [] is optional. 4791 The files used by tinker to create peptide can be used. 4792 Molden will remember the last amino acid added, so that 4793 new partial sequences can be added without selecting an 4794 atom to which it should be attached. 4795 When ready you can write it out as a PDB file, in the 4796 "Molden Control" window click "write" select "PDB". 4797 You can also write it as a tinker charm file, close the 4798 ZMAT-editor, click with the middle mouse button on an atom 4799 this will bring up the "Atom Attributes Window", click on 4800 The Force Field button and select "Tinker Charmm", now click 4801 on the write button int the "molden Control" window and 4802 select "Tinker". 4803 4804 4805Tue Aug 25 4806 - Fixed bug that let molden crash on certain pdb, tinker 4807 charmm files. 4808 4809 4810Tue Aug 11 4811 - Added support for Gaussian98 4812 - Molden now adds hydrogens to the amino acids and 4813 nucleotides of a PDB entry. 4814 - Added checking to user selection of atom types, 4815 for Tinker MM3 aand Tinker Charmm. 4816 4817 4818 Molden3.3: 4819 4820Thu Jul 23 - Added actinide elements, to atoms property editor 4821 - Fixed small bug which wrongly switch label button 4822 when FFtype was selected. 4823 4824Wed Jul 22 - Fixed bug in code to deal with ADF orbitals 4825 (Fabio Mariotti) 4826 - Gamess-uk/us uses different sequence of F orbitals 4827 than gaussian, molden always did the gaussian way, 4828 corrected. 4829 4830Mon Jul 20 4831 - Fixed small bug which prints lots of arrows on a molcular 4832 postscript plot when normal coordinates are available. 4833 - the ADF routine assumed exponents and normalisation 4834 constants read in from a molden format file as written 4835 by the ADFrom program to be in atomic units, this was 4836 not the case, the routine has been adapted. 4837 4838Tue Jul 14 4839 - By default molden always tries to make a z-matrix if 4840 there is none, occasionally it will have to add a 4841 dummy atom to accomplish this. This could cause 4842 problems reading some of the frequencies of a frequency 4843 job. Noe Fixed. 4844 4845Mon Jul 13 4846 - The window that lets you edit forcefield types, 4847 is now brought up when you select the label "ForceF.Type" 4848 When you click an atom with the middle mouse button 4849 as before this window is also popped up, but in addition 4850 the labelling is set to "ForceF.Type" 4851 - When using "Optimise" from the z-matrix editor it 4852 checks wether atoms typing has already been done. 4853 - Added some tinker forcefield parameters for acids, and esters 4854 to the .key file written when selecting "Optimise with Tinker" 4855 4856Wed Jul 8 4857 4858 - Added almost all spacegroups. 4859 - for molecules with no crystal information, it will 4860 be generated when you click on the CELL icon 4861 - Added reading of biosym arc files, use the movie 4862 and next button in combination with the "Geom. Conv." 4863 button. 4864 - Under the CELL icon, option "edit cell parameters"; 4865 you can now change the spacegroup of the cell 4866 - FDAT files containing multiple entries can now 4867 be viewed with the "Next" button. 4868 - Added "fit multipoles" under the surface icon 4869 (molden has to be compiled with "make molden.mpfit" 4870 for this option) 4871 - Added "Optimise xtinker" option under the CELL icon 4872 this writes input files for and executes an adapted version 4873 of xtalmin, an crystal structure optimiser from the tinker 4874 suite of programs. Adaptation by Wijnand Mooij, not yet 4875 available in the tinker distribution. 4876 4877Mon Jun 15 - Added plotting of distance monitors to postscript 4878 - Added more types for tinker mm3, automatic assigning 4879 still restricted to the old types. 4880 4881Thu Jun 11 - Added writing of Chemx(CSSR) files. 4882 4883 IMPORTANT !!!!!!! 4884 4885 - Fixed BUG in reading GAUSSIAN94 frequency outputs. 4886 It was introduced on 11 april 1998. 4887 4888Wed Jun 3 - Added Scrollable scrollbars 4889 - Added atom dynamic typing, click with the middle 4890 mouse button on a atom. 4891 4892Tue May 19 - Fixed a bug in molden.f which caused some compilers 4893 not to compile it. (Introduced at Thu May 14) 4894 4895 - Writing of animated vibrations in VRML2.0: 4896 4897 molden -w3 test/mopac.freq 4898 4899 Click "Norm. Mode" button, select a frequency, say 11 4900 a file "freq11.wrl" will have been written now. 4901 4902Thu May 14 - Added routine to fit multipoles to the electrostatic 4903 potential, stuff written by Wijnand Mooij 4904 (w.t.m.mooij@chem.ruu.nl), use keyword 'MPFIT' 4905 together with keywords described in file 'mpolefit.f' 4906 type 'make molden.mpfit' in the source directory to 4907 add this feature to molden. 4908 4909 - The new Gamess-US prints frequencies a little different 4910 which caused molden not to display the right frequencies 4911 this is solved 4912 4913Wed May 6 4914 4915 - Milan Hodoscek (xvibs) supplied code to plot 4916 normal coordinates as arrows in the postscript 4917 plot. EG: molden test/gaussian.freq 4918 click on Norm. mode button, choose the frequency, 4919 then click on Norm. mode button again, now click the 4920 postscript button. You can use the -s commandline flag 4921 to scale the amplitudes (eg: molden -s4.0) 4922 4923Mon Apr 27 4924 4925 - Improved the writing of VRML2.0 animations. 4926 These are invoked by: 4927 4928 molden -w3 geometriesfile 4929 4930 Then clicking the "Movie" button. At completion 4931 the VRML2.0 file 'movie.wrl' is written. 4932 It include a file via the WEB: 4933 4934 http://www.caos.kun.nl/~schaft/molden/wrl/animator.wrl 4935 4936 You can edit the movie.wrl via and subtitute the 4937 EXTERNPROTO declaration by the contents of animator.wrl. 4938 4939 Other adjustable parameters are the size of the animation 4940 window: Window [2,1] (Within the DEF MOLDEN_ANIMATOR 4941 definition). The cycleInterval in DEF MOLDEN_TIMER 4942 this is the time the animation should take. 4943 4944Wed Apr 15 4945 4946 - Added possibility to 'read' and 'write' basis set 4947 3D grids, a file 3dgridfile is created. 4948 4949 - Added choice of solid molecule draw: 4950 4951 "molden radii" (The old molden solid) 4952 4953 "vdwaals radii" 4954 4955 This on user requests. 4956 4957 4958Tue Apr 14 4959 4960 - Added reading of BOYS localised orbitals for Gamess-US 4961 4962Fri Apr 3 4963 4964 - The non Xwindows version of molden now works again 4965 4966 - Crystal visualisation support for chemx .cssr format 4967 and biosym .car files 4968 4969 - Through the Z-matrix editor you can build z-matrices 4970 which have translation or screw-axis symmetry. 4971 Read in the repeating unit, then click on 4972 4973 "Substitute atom by Fragment" 4974 4975 pick "Periodic", pick "Translation" or "screw-axis", 4976 specify the number of repeats. 4977 4978Mon Mar 23 4979 4980 - Support for the new(?) gamess_us PC version is 4981 has been added. 4982 4983 - Added animation of z-matrix variables. 4984 4985 - Added writing of POVRAY files 4986 4987Fri Feb 13 4988 4989 - enabled atonnumbering in postscript printing 4990 4991 - Electrostatic potential mapped to an isodensity 4992 surface is now possible. Also charges derived this way. 4993 4994 - Writing and reading of surfaces. 4995 4996 - Orbitals can be displayed as surfaces as well 4997 4998Tue Jan 27 4999 5000 - Enabled writing of 'ATOM' records in the PDB 5001 format. 5002 5003 - Enabled writing of Tinker Charmm files 5004 5005 - Postscript files written by molden, now allow 5006 the turning of of the zero contour 5007 5008 - Molden Postscript supports non solids drawings and 5009 shading on these sticks 5010 5011Fri Jan 9 5012 5013 - Added posibility to create a super cell 5014 5015 - Added read/write support for the crystallographic 5016 SHELX format (LATT 3, not yet supported) 5017 5018Thu Jan 8 5019 - Constants read in from the constants section of a 5020 gaussian/gamess-uk input file are flagged as such 5021 in the z-matrix editor, constants which have other 5022 variables linked to it, are written to the constants 5023 section of an gaussian/gamess z-matrix 5024 5025Wed Jan 7 5026 5027 - Fixed small bug in the gaussian output reading routine. 5028 When reading frequency output and encountering a 5029 'exceeding maxnum of orbitals' condition, the wrong 5030 coordinates were read. 5031 5032Fri Dec 5 5033 5034 - You can now specify the order of atoms in which a 5035 Z-matrix is to be created 5036 5037 - When working with files which contain crystal information 5038 (FDAT,MOL2,MSF) it is possible to map a z-matrix on file 5039 onto the cartesian coordinates. Your z-matrix file has 5040 to contain extra mapping information, so after the 5041 Z-matrix itself you have to supply the keyword 'map' 5042 followed a line per z-matrix atom which indicates 5043 to which atom it corresponds in the cartesian file. 5044 The name of this special Z-matrix file has to be 'mapfile'. 5045 You then start molden with the commanline flag -Z: 5046 5047 molden -Z test.fdat 5048 5049Mon Nov 24 5050 5051 - removed bug introduced a week ago, that messed up the 5052 connolly surfaces 5053 5054 - Added distance monitors 5055 5056 - Added editing of cell parameters. 5057 5058 - Added the possibilty to align two structures: 5059 5060 Read in stucture 1. 5061 Click the align icon in the center of the molden control 5062 window. Then supply the filename of the file containing 5063 structure2. Now use the standard ways of rotation,translation 5064 and zoom in/out (z-translation) to align stucture2 to 5065 structure1. You can also use the origin icon to change 5066 the center of rotation in structure2. 5067 You can switch between rotating both structures or 5068 structure2 by using the Esc key. 5069 Use the Tab key to align by selecting three couples of 5070 atoms (a couple = atom structure1 (red), atom structure2 5071 (white) 5072 5073 - Reading Support for the tinker .xyz format (mm3/charmm) 5074 5075 - It is now possible to work with crystals and change 5076 the position and orientation of the packed molecuul 5077 via the "Cell Rot On/Off" option under the cell icon. 5078 You can switch between rotating both structures or 5079 structure2 by using the Esc key. 5080 At the same time you can change the packed molecule itself 5081 via the z-matrix editor. 5082 5083 - Molden can now write input files for the Crystal95 5084 package. Basis sets of previous read in gamess/gaussian 5085 jobs are transferred to the Crystal95 input. 5086 Works of course only on fdat files and mol2/msf files 5087 containing crystal structures. 5088 5089 - molden -f pdbfile 5090 would create connectivity from scratch, however the 5091 HETATM records where not dealt with correctly. 5092 5093 - You can change 14 of the colors of the color palette 5094 "molden -r colorfile", where colorfile could be: 5095 5096 atom color(1-15) VandeWaalsRadius, (- = skip) 5097 background color(1-15) 5098 palette red #CF54FD ... (14 colors) 5099 5100 You can continue the last line on the next line when using 5101 the "\" character. You can use color names or Hex red-green 5102 -blue triplets 5103 5104Wed Nov 5 5105 - Added more spacegroups for use with mol2/msf files. 5106 (100 spacegroups supported) 5107 5108 - Improved crystal building code 5109 5110 - Support for Gamess-US IRC files 5111 5112 - Electrostatic potential due to point charges can 5113 be calculated/displayed on a connolly surface 5114 See Surface icon. 5115 5116 - On mopac output the ESP charges are read in when available. 5117 5118 - Writing of simple pdb files, via the 'HETATM' record. 5119 5120 - Fixed a bug that caused variable names such as 'e1', 'd1' 5121 in a z-matrix input to be not handled correctly. 5122 Bug was introduced with the introduction of the molden format. 5123 5124Mon Oct 27 - Introduction of the molden_format 5125 5126 - fix of molden format on linux 5127 5128 Molden3.2: 5129 5130Fri Oct 24 - Introduction of the molden_format, have a look at 5131 the "write" button. 5132 5133 - Normal modes with a sequence number greater than 99 5134 where not handled correctly 5135 5136 - The background color can be set via the molden -r 5137 flag, see molden -h; molden -r 5138 5139Mon Oct 13 - Gaussian Beta Orbitals were not always visible 5140 specially when read of a checkpoint file: 5141 5142Fri Oct 10 - Support for ADF, an intermediate program which 5143 reads ADF's tape21 can produce files readable 5144 by molden. This program was developed by Fabio Mariotti 5145 from Prof. Alessandro Bencini group in florence. 5146 5147 This intermediate program will eventually become part 5148 of the molden distribution, but since it is still 5149 under development, you should contact Prof. Bencini: 5150 5151 Prof. Alessandro Bencini 5152 Universita di Firenze 5153 Dipartimento di Chimica, Via Maragliano 75/77 5154 50144 Firenze, Italia 5155 5156 Tel: 39-(0)55-354841 5157 e-mail: sandro@chim1.unifi.it 5158 bencini@dada.it 5159 5160Wed Oct 8 - Fixed bug in Gamess-UK submit job scheme, the 5161 proper 'vectors' option was not always chosen. 5162 5163 - The Postscript color of the unit cell is now black 5164 per default, it can be changed by in the postscript 5165 file by setting /cellcol 5166 5167Wed Sep 24 - Added spin density for UHF calculations 5168 Use keyword SPINDENS together with IPSI=0 5169 5170 - Improved dmarel interface 5171 5172 - Removed multiple expose events on the zmatrix editor 5173 5174Mon Sep 8 5175 - more Gamess-UK version 6.0 support 5176 5177Fri Sep 5 5178 5179 - removed bug introduced day earlier, resulting 5180 in an floating exception on at least Linux 5181Wed Sep 3 5182 5183 - Gamess-UK version 6.0, added first support. 5184 5185 - Adapted postscript driver to handle editing of 5186 atom display radii. 5187 5188Thu Aug 28 - Enhanced atom color editor to atom property editor 5189 Now color, vdw and display radii can be altered. 5190 5191Thu Aug 21 5192 - Added Submitting of Gamess-UK Jobs. 5193 GAMESS_ROOT has to be set and the 'rungamess' script 5194 must be operational. 5195 5196Mon Aug 18 5197 - Added atom color editor. 5198 5199Fri Aug 15 5200 5201 - Removed bug which when molden was started without 5202 a file name would cause the molden control window 5203 to never pop up, certainly on AIX. 5204 5205 - Gamess-US: when using print options to print 5206 'AO MULLIKEN POPULATIONS IN EACH MOLECULAR ORBITAL' 5207 molden didnt read the occupancies correctly, 5208 resulting in the density to be calculated to low, 5209 and mulliken charges to be incorrect, orbitals ok. 5210 Fixed it. 5211 5212 - Added Submitting of Mopac Jobs, still very primitive. 5213 MOPAC_ROOT has to be set 5214 5215Mon Aug 11 - Removed small bug whith respect to the PLANE/ROT 5216 versus LINE/CENTER keywords. 5217 Using the PLANE keyword the orientation of the calculated 5218 rectangle of points is such that, the first atom specified 5219 with the PLANE keyword together with the center of the 5220 plot lie parallel with Y-plot axis, when LINE/CENTER 5221 or even ROT is used this scheme is abandoned. 5222 5223Wed Jul 23 - Added Submitting of Gaussian Jobs, still very primitive. 5224 5225Thu Jul 17 - Fixed bug that was dormant but became serious 5226 on a few platforms after introducing reading of mol2 5227 file on July 13. Files would not be correctly recognized. 5228 5229Wed Jul 16 - Added writing of tinker .xyz files. 5230 5231 - Added under "XYZ->curr.zmat" in the Z-matrix editor 5232 the possibility to optimise a structure with, sybyl 5233 quanta or tinker. 5234 The corresponding environment variable has to be set 5235 first (TA_ROOT, QNT_ROOT or TNK_ROOT) 5236 TNK_ROOT is not used by tinker itself, but molden needs 5237 it. (eg: setenv TNK_ROOT /compchem/tinker) 5238 The mm3 tinker parameter set will be used. 5239 Running quanta is shakey. 5240 5241 - Removed a bug that applied to Z-matrices automatically 5242 generated for XYZ files, changing variables in the Z-matrix 5243 would screw up the molecule. 5244 5245Fri Jul 4 - Added writing of Quanta/Charmm MSF files. 5246 5247 - Added atom row containing AG etc. in z-matrix editor. 5248 5249Tue Jul 1 - Added reading of Quanta/Charmm MSF files. 5250 5251 - You can now optimise you molecule with sybyl 5252 from the z-matrix editor. The environment variable 5253 TA_ROOT has to be set first. Choose the "XYZ->curr. zmat" 5254 button. 5255 5256Wed Jun 25 - Removed two bugs by which seemingly only the 5257 OpenVMS version was affected. 5258 5259Mon Jun 23 - The tolerence for partioning multipole expansion 5260 in symmetric molecules was to low, leading very 5261 occasionally to wrong multipoles, for higly symmetric 5262 molecules. Fixed it. 5263 5264Fri Jun 13 - Incorporated reading and writing mol2 files. 5265 For protein just coordinates are read. 5266 Writing of Mol2 is very primitive, with respect to 5267 atom types, and type of bonds is always single. 5268 But you can convert fdat to mol2 files this way, 5269 including charges, just first calculate charges on 5270 a job with the same atom order as the fdat file, 5271 then read in the fdat file and write mol2 (you will 5272 find it under the z-matrix editor, cartesian coordinates. 5273 Only the top-ten spacegroups have been incorporated, 5274 so 90 % of crystal structures will be read. 5275 5276Wed Jun 4 - Fixed bug introduced Fri May 30, affecting the proper 5277 writing of zmatrices. 5278 5279 - Fixed also some bug related with "delete line" in the 5280 z-matrix editor, having to do with maintaining the right 5281 status of an internal variable(=constant,=variable,=linked) 5282 5283 - In mopac DRC calculations the potential energy is now 5284 picked up. 5285 5286Fri May 30 - Rotation around the z-axis is now possible in both 5287 directions, clicking the mouse in the middle of the 5288 screen will give positive rotation, doing the same 5289 while holding down the Control or Shift key will 5290 give negative rotation 5291 5292 - Molden now supports writing of VRML2.0. 5293 Apart from the keyword VRML you can now use VRML2.0 5294 The -W commandline flag does the same. 5295 The various VRML buttons now let you choose between 5296 VRML1.0 and VRML2.0. 5297 The -w commandline flag now knows an option 3. 5298 When the movie button is pressed a VRML2.0 animation 5299 is written (movie.wrl). This can be viewed with a VRML2.0 5300 compliant browser such as Silicon Graphics Cosmoplayer 5301 plug-in (free available, also fro PC's). Clicking on 5302 the molecule will start the animation. 5303 5304 - typing "g" in the display screen will let you read in 5305 and XYZ file which will be mapped onto the current 5306 z-matrix, provided the number and the order of the elements 5307 is the same in both. 5308 5309Tue May 27 - Added interactive choice between mono and color postscript 5310 5311Fri May 23 - Added Pasting of strings capability to query boxes 5312 (For now button 3 will do this) 5313 5314 - The interactive calculations of: 5315 5316 True ESP derived charges (Very Slow) 5317 DMA esp derived charges 5318 Mulliken Charges 5319 5320 Via the Surface button. 5321 5322Thu May 22 - Removed a small bug in calculating the multipole 5323 derived electrostatic potential 5324 5325Fri May 16 - Charges are printed in postscript when the label 5326 "atom+charge" is active 5327 5328Wed May 14 - VRML of the elctrostatic potential "space" plots 5329 are now handled correctly. 5330 5331Tue May 6 - The Z-matrix scrollbar can now be clicked it, it 5332 will trigger pageup or pagedown movement. 5333 5334Fri May 2 - electrostatic potential on a connolly surface: 5335 5336 When clicking on the color level rectangle in the 5337 upper right corner with the second (or middle) mouse 5338 button you can change the colors used. 5339 5340 - Added keyword DMACH to calculate charges fit to 5341 Distributed Multipole Derived electrostatic potential. 5342 5343Tue Apr 29 - the true or multipole derived electrostatic potential 5344 on a connolly surface via keyword file now includes a 5345 postscript plot (-C to generate color postscript): 5346 5347 molden -C molin > molden.out 5348 5349 For the true electrostatic potential: 5350 5351 molin: 5352 ---------------------------------------------------------- 5353 title 5354 file=test/gamess_us.h2o_631g_opt.out postscript vdws elpot 5355 ---------------------------------------------------- 5356 5357 The new keywords XANG,YANG and ZANG controls the 5358 orientation viewed, usage XANG=45 (45 degrees) 5359 5360 - added the EST parameter set for writing input for the DMAREL 5361 program. (molden -e) 5362 5363 - added a button "H" to undisplay hydrogens, this is handy 5364 in combination with the CSD fdat files when displaying 5365 multiple cells. Getting rid of the hydrogen gives a 5366 clearer view of the crystal packing 5367 5368 - Dummy atoms will no longer be displayed in postscript 5369 molecule plots. 5370 5371Thu Mar 13 - Molden could already calculate the true or multipole 5372 derived electrostatic potential on a connolly surface, 5373 also VRML could be generated for this but only 5374 interactively, this can now be done with keywords: 5375 5376 molden molin > molden.out 5377 5378 For the true electrostatic potential: 5379 5380 molin: 5381 ---------------------------------------------------------- 5382 title 5383 file=test/gamess_us.h2o_631g_opt.out vrml vdws elpot 5384 ---------------------------------------------------- 5385 5386 For the multipole derived electrostatic potential: 5387 5388 molin: 5389 ---------------------------------------------------------- 5390 title 5391 file=test/gamess_us.h2o_631g_opt.out vrml vdws 5392 ---------------------------------------------------------- 5393 5394 A file molden.wrl will be written. 5395 5396 5397Wed Mar 12 - Added ability to display a cell with an Xmol xyz 5398 cartesian file: 5399 5400 After regular atoms add cell points, valid 5401 labels: 5402 5403 OO,OA,OB,OC,AB,BC,AC,ZZ 5404 5405 These cell points must be included in the number 5406 of atoms. 5407 5408 - The geometry convergence window together with 5409 the movie button have been updated: 5410 5411 You can now stop a movie by clicking "first", "next" 5412 or by selecting a point in the geometry window. 5413 The tick marks are adapted so as not to overlap 5414 when there are a large number of points. 5415 5416 - added a file epint.f.g77, gnu fortran has problems 5417 compiling the original epint.f. So before typing 5418 "make", copy epint.f.g77 to epint.f. 5419 5420 - Linux2.* has problems with Molden (And Gaussian94) 5421 this probably due to an operating system bug affecting 5422 memory management. 5423 5424 - Removed bug in calculating the q31s octupole moment 5425 (Only when using D-functions) 5426 5427 - Added commandline flag to keep the order of atoms 5428 when creating a z-matrix from cartesian coordinates 5429 5430 molden -A 5431 5432 - Molden now writes an file "esp.xyz" when doing an 5433 ESP charges calculation, it contains the atoms +charge 5434 in xyz-coordinates 5435 5436 - added support for Gamess-UK rhf localised orbitals. 5437 5438 - Added beta-test support for DMAREL, a package that 5439 can calculate lattice energies from a multipole 5440 expansion. 5441 5442 New Commandline flags: 5443 5444 -E DMAREL input: use coordinates from multipoles 5445 -i opt fdat files: 5446 opt=1 standardise H-C, H-N 5447 opt=2 1 + standardise phenyl rings 5448 5449 Other Relevant flags: 5450 5451 -A Keep order of atoms when creating a Z-matrix 5452 -D opt DMA mode: 5453 0 = atomic sites only (default) 5454 1 = atomic+halfway-bond sites 5455 5456 When creating a z-matrix for an optimisation run to be used 5457 with DMAREL you must keep the order of the atoms as in the 5458 CSD FDAT file and turn of symmetry to keep it this way: 5459 5460 molden -A -i 2 azijnzuur.fdat -> azijnzuur.zmat 5461 5462 To use the optimised coordinates instead of the FDAT 5463 coordinates in writing DMAREL input, use 5464 5465 molden -E azijnzuur_opt.out azijnzuur.fdat 5466 5467 if you want to use bondcenters as well, 5468 5469 molden -E -D 1 azijnzuur_opt.out azijnzuur.fdat 5470 5471 If you want to use fdat coordinates with bondcenters, 5472 5473 molden -D 1 -i 2 azijnzuur.out azijnzuur.fdat 5474 5475 In molden click on the surface button, choose 5476 "Multipole Derived", then read in the FDAT file, 5477 click on the "Cell" button and choose "Write DMAREL" 5478 a file "dmain" will be created. 5479 5480 5481Wed Feb 12 - In the density mode you could zoom in on the plot 5482 with the second mouse button, sometimes old plot 5483 were mixed with new plots, fixed it. 5484 5485Tue Feb 11 - GAMESS-US: when using the HSSEND keyword to do a 5486 normal vibration analysis at the end of a geometry 5487 optimisation, the default is to display geometry 5488 optimisation information, but molden -H will 5489 trigger visualisation of normal vibration analysis. 5490 - GAMESS-US: when imaginairy frequencies were present 5491 molden would skip the rest of the normal modes in 5492 that line of the output. 5493 5494Mon Feb 10 - Fixed bug in the 'space' mode of orbital plotting 5495 A space plot consists of the density/orbital-amplitude 5496 plotting and the plotting of the molecule in the 5497 stick mode. If the density/orbital-amplitude was to low 5498 in a slice then also the part of the molecule in this 5499 slice was not plotted. (This did not affect the VRML 5500 space filling plots) 5501 5502Wed Dec 18 - Incorporated writing of inputfiles for aresp: 5503 Using the keyword 'aresp' will let molden write 5504 the files 'resp.in' and 'esp.in' 5505 Example keyword file: 5506 5507 line1: test esp 5508 line2: file = water.out espch debug aresp 5509 5510 - The keyword occu dint work correctly, fixed 5511Wed Dec 11 5512 - Molden can now do gaussian natural orbitals as generated 5513 by the keywords: 5514 pop=(naturalorbitals) gfinput iop(6/7=3) 5515 - Molden with Gaussian94 and outputs with only cartesian 5516 coordinates would say 'reference to an undefined center' 5517 but would still work correct, solved 5518 5519Mon Dec 9 - Molden didnt recognise certain Gaussian94 UHF jobs. 5520 Resulting in only one set of orbitals being displayed 5521 5522 - Dihedrals with a negative value where not properly 5523 written as constants in write zmatrix 5524 5525 - In zmatrix editor in the line drawing plot mode 5526 the molecule become invisible after adding line two 5527 this because th view direction was along the axis of the 5528 molecule, fixed it. 5529 5530 - some mopac output reads would hang 5531 5532 - added a little more control over the postscript file 5533 5534 5535 5536Fri Oct 18 Removed following bugs: 5537 5538 - GAMESS-US input files with zmatrix and point group C1 5539 failed 5540 5541 - PDB file containing only non-protein and non-rna werent 5542 handled well 5543 5544 - FDAT files with NRAD=0 failed 5545 5546Thu Oct 17 Removed following bug, when building a structure 5547 with the zmatrix editor the display would show the mirror 5548 image of the real structure. When writing out this structure 5549 and then reading it back in to molden the structure would 5550 be displayed in the right way. 5551 5552Wed Oct 9 Added the possibility to do a Distributed Multipole Analysis 5553 and the calculation of Mulliken charges. 5554 For now, Mulliken charges are calculated only for single point 5555 Gamess/Gaussian runs. 5556 The Distributed Multipole Analysis can be activated by use 5557 of the keyword "MOLPOT". Interactively it can be activated 5558 either from the "molden control window" by pushing the 5559 "surface button" (The 6th icon in the middle of the window) 5560 or pushing the "Dens. Mode" button and consequently choosing 5561 the plot function "Elec. Pot" in both cases the user is then 5562 presented with the choice between the true electrostatic 5563 potential and the electrostatic potential derived from a 5564 Multipole expansion. The latter is an order of a magnitude 5565 faster than the first. 5566 5567 Three types of DMA are available, they can be selected via 5568 the "-D opt" commandline flag, where opt can have the values: 5569 5570 5571 0 = atomic sites only (default) 5572 1 = atomic+halfway-bond sites 5573 2 = no shift of overlap dens. of conn. atoms 5574 5575 NOTE: In previous versions the keyword "MOLPOT" was used 5576 with a DMA analysis read from a Gamess-UK outputfile. 5577 Use keyword "RDMULT" to get the old functionality. 5578 5579 5580 5581 5582 5583 5584 Molden3.1: 5585 5586Thu Aug 29 Calculating the Laplacian via a keyword file, core dumped 5587 It has been resolved. 5588 5589Thu Aug 22 - When visualizing csd fdat files in the "multiple cells" 5590 problems arose when there were Hydrogen bonds present. 5591 This has been resolved. 5592 5593Wed Aug 21 - Support for the laplacian of the electron density, 5594 (the trace of the hessian). 5595 Two commandline flags were introduced to aid the 5596 space type of plots with the laplacian. 5597 5598 -L display both neg. and pos. contour in space 5599 plot of the laplacian. Default only the value 5600 specified with "space=value" will be rendered. 5601 -1 use only the lower half of the cubic grid 5602 used for the space type plot 5603 -2 use only the upper half of the cubic grid 5604 used for the space type plot 5605 5606 The latter two were introduced to increase the visibility 5607 of the inner (enclosed by other surfaces) surfaces. 5608 5609Thu Jul 25 - Corrected a bug which made you have to click buttons 5610 twice 5611 5612Fri Jul 12 - Corrected problem with postscript 5613 5614 - Electrostatic potential on connolly surface added. 5615 Activated by Clicking on the appropriate icon in the 5616 middle of the molden control window. 5617 Clicking on points of the surface brings of a popup 5618 window with its electrostatic potential value. 5619 In the upper right corner of the screen there is a 5620 color code rectangle, clicking in it lets you change 5621 the increment value between different colors. 5622 The 'molden -G 0.5' commandline flag controls the 5623 spacing between the lines that make up the connolly 5624 surface. 5625 5626 - Added the capability to write VRML 5627 (molden -V filename, specifies density VRML file, 5628 default: molden.wrl) 5629 5630 - You can now create a Z-matrix with symmetry, use 5631 mouse button two in the zmatrix editor, to: 5632 - link variables 5633 - to make constants 5634 - to mark or unmark 5635 5636 Molden3.0: 5637 5638Thu May 23 - Corrected problems on some platforms with the fdat format 5639 and the reading of XYZ format without the -X flag 5640 5641Wed May 22 - Rotation in the density window is now attached to button 5642 one, rotation will proceed until the button is released, 5643 cropping is now attached to button two 5644 5645Wed May 15 - Molden now also recognizes XYZ format without the -X flag 5646 - zoom in/out will proceed untill the button is released 5647 5648Fri May 10 - Better encapsulated postscript 5649 - Better hydrogen bond display for PDB files 5650 - support for hydrogens on RNA/DNA pdb. 5651 - molden -r fname: read file with per line; 5652 atom color(1-15) VandeWaalsRadius, (- = skip) 5653 - molden -w opt: write all points of a movie to a file: 5654 opt specifies format; xyz(=1) zmat(=2,mopac) 5655 5656Thu Apr 25 - Increased support for CSD .fdat files. 5657 5658Wed Apr 17 - Support for mopac93/6.0 irc output 5659 - gamess-uk inputfiles with no variables/constants oke now 5660 - added command line flag for switching off automatic 5661 cartesian -> zmatrix conversion; "molden -a" 5662 5663Tue Apr 09 - Some platforms dont support the "logical*1" 5664 - Enhanced cartesian -> Z-matrix conversion 5665 5666Tue Mar 29 - Support for mopac6.0/7.0 force runs. 5667 - Allow to set the background color, via palette icon. 5668 5669Tue Mar 28 - Support for CSD .fdat files, molden -S will generate 5670 symmetry positions and a unit cell. 5671 - xmol files that used scientific notation (1.0e05) 5672 are now also handled well 5673 5674Tue Mar 19 Mopac input files didnt show up in the z-matrix editor 5675 fixed it. You read mopac input files as fragment in the 5676 z-matrix editor. 5677 5678Fri Mar 15 Added built in GIF writing capability, dropping the use 5679 of the external "convert" program from ImageMagick 5680 5681Wed Mar 13 Extended and improved the rotation of the molecule, 5682 holding the mouse button down in the center of the graph 5683 will invoke rotation around a z-axis 5684 5685Tue Mar 5 A VERY serious bug effected the calculation of the 5686 electrostatic potential and esp charges with Gamess-US/UK 5687 output. (It was introduced with Gamess-US support nov. 95) 5688 esp's from Gaussian were unaffected !! 5689 5690 - ESP charges: introduced keywords AXIS-X,AXIS-Y,AXIS-Z 5691 They the define the principle axis used in constructing 5692 the atomspheres which make up the connolly surface. 5693 Sometimes necessary when you want to reproduce symmetry. 5694 5695Wed Mar 4 - support now for dih, -dih variable use when reading 5696 Gamess/Gaussian inputfiles. 5697 - With Gamess-UK optimise jobs molden would show 5698 orbital energies of the first point, instead of the last 5699 point, fixed. 5700 5701Mon Feb 26 A number of bug fixes and new features, see also 5702 The history of molden2.9: 5703 5704 - Added color postscript for Density Display. 5705 Triggered by commandline flag -C 5706 5707 - Removed bug that would mess up the EUCLID display 5708 when clicking the Postscript button. 5709 5710 - considerably enhanced reading and displaying of PDB 5711 structures. 5712 5713 Helix, beta secondary structure information, will 5714 by default be read from the PDB file, if not available 5715 Molden will calculate secondary structure information. 5716 Use "molden -g" to allways force the latter. 5717 From the "Residue Command" window this information can 5718 be edited. 5719 The color postscript rendering of PDB structures has 5720 also been dramatically improved. 5721 Molden also lets you display parts of the molecule as 5722 a connolly surface. 5723 5724 - molden now supports pure F/D-functions (7f,5d) 5725 5726 - GAUSSIAN: molden now also read orbitals from dft 5727 calculations. 5728 5729 - Added commandline flag -h, which prints the available 5730 options. 5731 5732 5733 5734 5735 Molden2.9: 5736 5737Thu Feb 22 - Added color postscript for Density Display. 5738 Triggered by commandline flag -C 5739 5740 - Removed bug that would mess up the EUCLID display 5741 when clicking the Postscript button. 5742 5743 - Made postscript file more suitable for customizing. 5744 5745Tue Feb 20 GAUSSIAN: molden now supports pure F-functions (7f) 5746 molden only used to read cartesian F (10f) 5747 (As with pure D, not yet for the electrostatic 5748 potential) 5749 With Gaussian92 and older in combination with 5750 ROHF all orbitals were printed, Molden now 5751 reads all the orbitals. 5752 5753Fri Feb 16 GAUSSIAN: the use of nosymm could lead to problems. 5754 Think I've tackled it now. 5755 Also the SCF convergence reading when 5756 "SCF Done: E(RB+HF-LYP)" was on the output 5757 could cause problems. 5758 5759Thu Feb 15 Changed default to Color Postscript for the molecular 5760 display. (Color postscript for the density display not 5761 yet implemented) Mono postscript can still be generated 5762 by use of the commandline flag -M (molden -M) 5763 5764Thu Feb 8 - Removed bug in postscript printing. 5765 - PDB: default is now to read secondary structure info 5766 from the PDB file, if there is non the info is 5767 calculated. Use "molden -g" to allways force the 5768 latter. 5769 5770Wed Feb 7 The postscript (color) rendering of protein structures from 5771 the PDB has considerably been enhanced 5772 5773Fri Feb 2 Removed small bug affecting only Ultrix versions of molden 5774 when displaying dummy atoms in the solid mode. 5775 Removed small bug affecting Ultrix,Solaris when adding 5776 a fragment in the Z-matrix editor when no line is selected 5777 5778Thu Feb 1 On the rs6000 (ibm,aix) molden sometimes gave annoying 5779 run time warnings, such as "C invalid decimal digit" 5780 5781Wed Jan 31 - GAMESS-US: 5782 With geometry optimisations, for each geometry point 5783 the z-matrix is read from the output. It used to be 5784 generated by Molden. To update the coordinates on screen 5785 with the coordinates belonging to the z-matrix, 5786 push "Aplly current changes to Z-matrix" 5787 Supplying "molden -u" will restore the old behaviour. 5788 5789 - Removed small bug which caused problems on 5790 a Gaussian optimise job on an already optimised 5791 geometry (vectors are still a problem in this case) 5792 5793Tue Jan 30 - Added connolly surface's for protein (PDB) viewing. 5794 - Added commandline flag to scale normal motions 5795 molden -s4 5796 will increase the amplitude of the vibrations times 4 5797 5798 Molden2.8: 5799 5800Tue Jan 25 - Removed small bug in the automatic z-matrix generation 5801 - GAMESS-US: not converged optimisations showed a last 5802 invalid point, rendering de energy plot useless. 5803 - Problems encountered when having more than 200 points 5804 in an optimisation or IRC have been dealt with. 5805 5806Tue Jan 23 Gaussian: molden used to generate its own z-matrix 5807 for the z-matrix editor (except gaussian input files) 5808 Now it retains the z-matrix on the outputfile. 5809 (except for "force jobs") 5810 5811Tue Jan 22 Removed small bug in displaying SCF convergence, SCF 5812 convergence of last point sometimes not displayed. 5813 5814Thu Jan 18 Provisionally supported gaussian 5d functions. 5815 (density only, electrostatic potentials not yet supported) 5816 5817Wed Jan 17 Removed a bug affecting the reading of gamess input files. 5818 5819Wed Jan 16 Added beta sheet solid rendering. 5820 5821Fri Jan 12 Added numbering to atoms on screen for the convenience 5822 of the Z-matrix editor (switch on label when in the 5823 zmat editor. 5824 5825 Added "substitute atom by fragment" capability in the 5826 zmat editor, you can also read a gamess/gaussian/mopac 5827 input file as fragment. 5828 5829 58301995 5831 5832 5833Thu Dec 21 Added nucleotide support when reading PDB files 5834 5835Thu Dec 20 Removed bug in z-matrix editor which yielded 5836 wrong guesses for bond distances for rare atoms 5837 Removed bug in z-matrix editor, which in case of a wrongly 5838 user supplied value and when the # of zmat lines was less 5839 than 9, would garble the zmat-editor screen. 5840 5841Thu Dec 7 Removed a bug which only affected the Sun solaris version. 5842 (In the z-matrix editor whilst adding the second atom) 5843 5844Tue Dec 5 MAJOR BUG FIXES: 5845 5846 - molden with GAUSSIAN94 UHF showed only alpha orbitals 5847 - GAMESS-US UHF geometry optimisation showed no orbitals 5848 5849Thu Nov 30 removed sleep call in inferr.f, caused problems on AIX,linux 5850 and openvms. 5851 Zmatrix editor now supplies the first fragments 5852 5853Wed Nov 29 On AIX molden hangs after pushing the "space" button, 5854 it was caused by a call to sleep, which should return 5855 after 2 seconds but it never returns, you have to 5856 deactivate this line in file inferr.f 5857 5858 GAMESS-US IMPORTANT BUGS: 5859 5860 - Scf-Convergence of GAMESS-US outputs would be empty 5861 when "* * * INITIATING DIIS PROCEDURE * * *" 5862 was on the output. Taken care of. 5863 5864 - fixed inproper reading of orbital occupancies. 5865 5866 - fixed incorrect handling of normal vibrations > 9 5867 5868Tue Nov 21 When entering the z-matix editor without having read a file 5869 first, an error occured while adding the second atom of a 5870 new z-matrix, removed it. 5871 Cleaned up z-matrix editor code for monochrome displays. 5872 Removed a bug in routine hidedr, only OpenVMS affected. 5873` Z-mat editor is a little more intelligent now. 5874 5875Fri Nov 10 Protein viewing: removed inconsistency in displaying hetatm 5876 records 5877 5878Mon Nov 6 Gaussian-94 users NOW should use iop(6/7=3) instead of 5879 iop(6/7=1), the latter option under g94 nolonger prints all 5880 occupied orbitals, the first prints all orbitals. 5881 5882Fri Oct 20 First beta support for Gamess-US 5883 And both alpha and beta orbitals (UHF runs) are now displayable. 5884 5885 5886 5887 Molden2.7: 5888 5889Mon Oct 9 Made minor changes to let the code compile on Linux, 5890 the user has to edit file inferr.f before compilation. 5891 5892Thu Sep 28 The distance,angle and dihedral button now display their 5893 output in a dedicated window. 5894 5895Wed Sep 27 Support of Gaussian94 output. 5896 Fixed bug introduced on Sep 11, which made the gamess 5897 vibration animation routines use the wrong set of coordinates. 5898 5899 5900 Molden2.6: 5901 5902Tue Sep 26 Support for pdb ambiguity amino acids, asx,glx,his 5903 and hydroxyproline (hyp). 5904 Also HETATM A.. are now recognised. 5905 Added popup box that lets you choose the color of your HETATM 5906 molecule. 5907 5908Fri Sep 22 Fixed an important bug introduced on Mon Sep 18. 5909 5910Mon Sep 18 The cartesian coordinates to z-mat converter now WILL 5911 produce a z-matrix for molecules containing 3 atoms on a line. 5912 5913Fri Sep 15 Added the capability to write cartesian coordinates from 5914 the Z-matrix editor. 5915 5916Thu Sep 14 Fixed a bug that lets molden crash on some systems, in the 5917 case of a molecule containing 3 atoms on a line. 5918 Fixed a few other unclarities in the z-mat editor, however 5919 the z-mat editor still needs a lot of work. 5920 The cartesian coordinates to z-mat converter will not 5921 produce a z-matrix for molecules containing 3 atoms on a line 5922 5923Mon Sep 11 Single point gamess calculations retain their user specified 5924 z-matrix in the z-matrix editor 5925 5926Thu Sep 7 For pdb files only: 5927 Made second display type for the solid helix default 5928 Added "neigh=r" command in the residu command window. 5929 Neigh looks for neighbours at distance r 5930 Changed "substrate" to "hetatm" in the molden control 5931 window, clicking it will lets you choose which hetatm molecules 5932 you want to display 5933 5934Tue Aug 1 Added second display type for the solid helix 5935 5936Mon Jul 24 Display of vibrations for mopac (tested on mopac93) 5937 5938Fri Jul 14 Incorporated calculation of charges fitted to the 5939 ElectroStatic Potential (ESP) on a series of connolly 5940 surfaces. (Only for gamess/gaussian) (see test/esp.txt) 5941 5942 5943 Molden2.5: 5944 5945Fri Jun 30 The compilation of xwin.c caused some problems on non-ansi 5946 compiler systems (hp,sun), fixed it. 5947 5948Thu Jan 26 Removed redundant code which made molden eat cpu when it 5949 should be idle. 5950 Apparently molden plotted inverted molecules, changed it 5951 5952Jan Improved lighting (At least for protein viewing) 5953 59541994 5955 5956Fri Oct 21 Made support for XMOL cartesian format. Use -X flag 5957 5958Thu Oct 20 Changed resolution of postscript molecule plotting, 5959 depending on number of atoms. (Plotting proteins was 5960 very slow) 5961 Eliminated trailing in rotating the molecule. 5962 Molden can now generate color postscript for the molecule 5963 display by using the -C flag. 5964 5965Tue Sep 22 ZMatrix editor implemented, incorporating a very rudimentary 5966 builder. 5967 5968 5969 5970 Molden2.4: 5971 5972Tue Aug 16 Scf/Geometry convergence graphs improved and will now 5973 display function value when cursor is over the graph point. 5974 clicking in the graph will bring up the current point for 5975 display 5976 5977Tue Aug 10 Added support for reading Gamess/Gaussian/Mopac inputfiles 5978 and Mopac/Ampac arc files. 5979 5980Mon Aug 1 Added listbox to select orbitals, made internal rearrangements 5981 for systematic handeling of queryboxes, listboxes 5982 Some query boxes now remain on the screen untill a toggle 5983 button is pressed 5984 5985Mon Jul 11 Gamess/Gaussian frequencies/Norm. Modes can now be displayed. 5986 5987 5988 Molden2.3: 5989 5990Mon Jun 27 Improved shaded plotmode & switched to fully 3D controls 5991 5992Tue May 17 Removed bugs on commandline parsing on some systems 5993 5994Tue Feb 1 handle gaussian92 scf convergence 5995 (turned on by #P in gaussian inputfile) 5996 5997Jan 20 Made molden pc X compatible 5998 5999Thu Dec 23 -c0.2 define depth of shading 0.0 is max, 1.0 is no shades 6000 6001Tue Dec 16 removed bug in the H-bond on screen display routine 6002 6003Wed Dec 15 -f with PDB files, forces connectivity to be build by molden 6004 by default connectivity between amino acid atoms are read 6005 from the PDB file and for all other atoms molden determines 6006 the connectivity 6007 6008Fri Dec 3 better handling hbond when more than one chain 6009 better spheres, and beter coloring with shade 6010 6011Thu Dec 2 Better atom selecting by cursor. 6012 perspective is now uniform from large to small molecules 6013 -p10.0 perspective flag 6014 6015Tue Nov 30 Added reading of binary mopac/ampac *.gpt files 6016 6017Fri Nov 26 -ofilename change the default plotfilename='plot' 6018 trying to put in spheres with real depth, not satisf. yet 6019 -d debug flag 6020 6021Thu Nov 25 bug out of getmul.f, by Dirk Huckriede 6022 6023Nov 10 Dec Alpha version, corrected problems in wrzmat.f 6024 6025========================================================================= 6026 6027 6028TODO: 6029 6030- improve zmat editor 6031 6032- Density Functional orbitals of Gaussian94 ? 6033 6034- Clean up handling of dummies 6035 6036- Third rotation axis. 6037 6038- Mopac IRC 6039 6040