1<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> 2<tr bgcolor="#FFFFCC"> 3<th align="left">Qualifier</th> 4<th align="left">Type</th> 5<th align="left">Description</th> 6<th align="left">Allowed values</th> 7<th align="left">Default</th> 8</tr> 9 10<tr bgcolor="#FFFFCC"> 11<th align="left" colspan=5>Standard (Mandatory) qualifiers</th> 12</tr> 13 14<tr bgcolor="#FFFFCC"> 15<td>[-infile]<br>(Parameter 1)</td> 16<td>infile</td> 17<td>Clean protein structure coordinates file</td> 18<td>Input file</td> 19<td><b>Required</b></td> 20</tr> 21 22<tr bgcolor="#FFFFCC"> 23<td>-chainnumber</td> 24<td>integer</td> 25<td>Number of the chain for which torsion angles should be calculated</td> 26<td>Integer 1 or more</td> 27<td>1</td> 28</tr> 29 30<tr bgcolor="#FFFFCC"> 31<td>-startresiduenumber</td> 32<td>integer</td> 33<td>First residue in chain for which torsion angles should be calculated</td> 34<td>Integer 1 or more</td> 35<td>1</td> 36</tr> 37 38<tr bgcolor="#FFFFCC"> 39<td>-finishresiduenumber</td> 40<td>integer</td> 41<td>Last residue in chain for which torsion angles should be calculated (1 = last residue)</td> 42<td>Any integer value</td> 43<td>1</td> 44</tr> 45 46<tr bgcolor="#FFFFCC"> 47<td>[-outfile]<br>(Parameter 2)</td> 48<td>report</td> 49<td>Output report file name</td> 50<td>(default -rformat table)</td> 51<td><i><*></i>.psiphi</td> 52</tr> 53 54<tr bgcolor="#FFFFCC"> 55<th align="left" colspan=5>Additional (Optional) qualifiers</th> 56</tr> 57 58<tr> 59<td colspan=5>(none)</td> 60</tr> 61 62<tr bgcolor="#FFFFCC"> 63<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> 64</tr> 65 66<tr> 67<td colspan=5>(none)</td> 68</tr> 69 70<tr bgcolor="#FFFFCC"> 71<th align="left" colspan=5>Associated qualifiers</th> 72</tr> 73 74<tr bgcolor="#FFFFCC"> 75<td align="left" colspan=5>"-outfile" associated report qualifiers 76</td> 77</tr> 78 79<tr bgcolor="#FFFFCC"> 80<td> -rformat2<br>-rformat_outfile</td> 81<td>string</td> 82<td>Report format</td> 83<td>Any string</td> 84<td>table</td> 85</tr> 86 87<tr bgcolor="#FFFFCC"> 88<td> -rname2<br>-rname_outfile</td> 89<td>string</td> 90<td>Base file name</td> 91<td>Any string</td> 92<td> </td> 93</tr> 94 95<tr bgcolor="#FFFFCC"> 96<td> -rextension2<br>-rextension_outfile</td> 97<td>string</td> 98<td>File name extension</td> 99<td>Any string</td> 100<td> </td> 101</tr> 102 103<tr bgcolor="#FFFFCC"> 104<td> -rdirectory2<br>-rdirectory_outfile</td> 105<td>string</td> 106<td>Output directory</td> 107<td>Any string</td> 108<td> </td> 109</tr> 110 111<tr bgcolor="#FFFFCC"> 112<td> -raccshow2<br>-raccshow_outfile</td> 113<td>boolean</td> 114<td>Show accession number in the report</td> 115<td>Boolean value Yes/No</td> 116<td>N</td> 117</tr> 118 119<tr bgcolor="#FFFFCC"> 120<td> -rdesshow2<br>-rdesshow_outfile</td> 121<td>boolean</td> 122<td>Show description in the report</td> 123<td>Boolean value Yes/No</td> 124<td>N</td> 125</tr> 126 127<tr bgcolor="#FFFFCC"> 128<td> -rscoreshow2<br>-rscoreshow_outfile</td> 129<td>boolean</td> 130<td>Show the score in the report</td> 131<td>Boolean value Yes/No</td> 132<td>Y</td> 133</tr> 134 135<tr bgcolor="#FFFFCC"> 136<td> -rstrandshow2<br>-rstrandshow_outfile</td> 137<td>boolean</td> 138<td>Show the nucleotide strand in the report</td> 139<td>Boolean value Yes/No</td> 140<td>Y</td> 141</tr> 142 143<tr bgcolor="#FFFFCC"> 144<td> -rusashow2<br>-rusashow_outfile</td> 145<td>boolean</td> 146<td>Show the full USA in the report</td> 147<td>Boolean value Yes/No</td> 148<td>N</td> 149</tr> 150 151<tr bgcolor="#FFFFCC"> 152<td> -rmaxall2<br>-rmaxall_outfile</td> 153<td>integer</td> 154<td>Maximum total hits to report</td> 155<td>Any integer value</td> 156<td>0</td> 157</tr> 158 159<tr bgcolor="#FFFFCC"> 160<td> -rmaxseq2<br>-rmaxseq_outfile</td> 161<td>integer</td> 162<td>Maximum hits to report for one sequence</td> 163<td>Any integer value</td> 164<td>0</td> 165</tr> 166 167<tr bgcolor="#FFFFCC"> 168<th align="left" colspan=5>General qualifiers</th> 169</tr> 170 171<tr bgcolor="#FFFFCC"> 172<td> -auto</td> 173<td>boolean</td> 174<td>Turn off prompts</td> 175<td>Boolean value Yes/No</td> 176<td>N</td> 177</tr> 178 179<tr bgcolor="#FFFFCC"> 180<td> -stdout</td> 181<td>boolean</td> 182<td>Write first file to standard output</td> 183<td>Boolean value Yes/No</td> 184<td>N</td> 185</tr> 186 187<tr bgcolor="#FFFFCC"> 188<td> -filter</td> 189<td>boolean</td> 190<td>Read first file from standard input, write first file to standard output</td> 191<td>Boolean value Yes/No</td> 192<td>N</td> 193</tr> 194 195<tr bgcolor="#FFFFCC"> 196<td> -options</td> 197<td>boolean</td> 198<td>Prompt for standard and additional values</td> 199<td>Boolean value Yes/No</td> 200<td>N</td> 201</tr> 202 203<tr bgcolor="#FFFFCC"> 204<td> -debug</td> 205<td>boolean</td> 206<td>Write debug output to program.dbg</td> 207<td>Boolean value Yes/No</td> 208<td>N</td> 209</tr> 210 211<tr bgcolor="#FFFFCC"> 212<td> -verbose</td> 213<td>boolean</td> 214<td>Report some/full command line options</td> 215<td>Boolean value Yes/No</td> 216<td>Y</td> 217</tr> 218 219<tr bgcolor="#FFFFCC"> 220<td> -help</td> 221<td>boolean</td> 222<td>Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose</td> 223<td>Boolean value Yes/No</td> 224<td>N</td> 225</tr> 226 227<tr bgcolor="#FFFFCC"> 228<td> -warning</td> 229<td>boolean</td> 230<td>Report warnings</td> 231<td>Boolean value Yes/No</td> 232<td>Y</td> 233</tr> 234 235<tr bgcolor="#FFFFCC"> 236<td> -error</td> 237<td>boolean</td> 238<td>Report errors</td> 239<td>Boolean value Yes/No</td> 240<td>Y</td> 241</tr> 242 243<tr bgcolor="#FFFFCC"> 244<td> -fatal</td> 245<td>boolean</td> 246<td>Report fatal errors</td> 247<td>Boolean value Yes/No</td> 248<td>Y</td> 249</tr> 250 251<tr bgcolor="#FFFFCC"> 252<td> -die</td> 253<td>boolean</td> 254<td>Report dying program messages</td> 255<td>Boolean value Yes/No</td> 256<td>Y</td> 257</tr> 258 259<tr bgcolor="#FFFFCC"> 260<td> -version</td> 261<td>boolean</td> 262<td>Report version number and exit</td> 263<td>Boolean value Yes/No</td> 264<td>N</td> 265</tr> 266 267</table> 268