Lines Matching refs:cmd
2 from pymol import cmd
16 cmd.delete("all")
18 … cmd.do("_ wizard message, Please wait while the %s example loads..., dismiss=0"%pretty_name)
20 cmd.refresh_wizard()
31 _self=kw.get('_self',cmd)
35 cmd.full_screen("off")
37 cmd.stereo("on")
38 cmd.set("sphere_mode","5")
100 file = cmd.exp_path(file)
108 cmd.set_session(self.get_sess("$PYMOL_DATA/big_demo/homology.pse"))
109 cmd.do("replace_wizard toggle, Homology Modeling")
113 cmd.set_session(self.get_sess("$PYMOL_DATA/big_demo/structure.pse"))
114 cmd.do("replace_wizard toggle, Structure Alignment")
115 cmd.set("seq_view_label_mode",1)
116 cmd.set("seq_view",1)
118 cmd.set("seq_view_label_mode",0)
119 cmd.set("seq_view",0)
123 cmd.set_session(self.get_sess("$PYMOL_DATA/big_demo/drugdisc.pse"))
124 cmd.do("replace_wizard toggle, Medicinal Chemistry")
126 cmd.set("sphere_scale",1.0)
130 cmd.feedback("disable","objectsurface","actions")
131 cmd.set_session(self.get_sess("$PYMOL_DATA/big_demo/flagellar.pse"))
132 cmd.set("sweep_mode",3)
133 cmd.set("sweep_angle",3)
134 cmd.rock()
135 cmd.do("replace_wizard toggle, Electron Tomography")
137 cmd.mstop()
138 cmd.rock(0)
142 cmd.set_session(self.get_sess("$PYMOL_DATA/big_demo/electro.pse"))
143 cmd.do("replace_wizard toggle, Computational Chemistry (Electrostatics)")
144 cmd.rock(1)
146 cmd.rock(0)
150 cmd.set("security",0)
151 cmd.set_session(self.get_sess("$PYMOL_DATA/big_demo/animate.pse"))
152 cmd.rock(1)
153 cmd.set("field_of_view",23)
154 cmd.rock(1)
155 cmd.set("sweep_mode",3)
156 cmd.set("sweep_angle",10)
157 cmd.set("sphere_mode",5)
158 cmd.do("replace_wizard toggle, Molecular Animation")
160 cmd.set("mesh_width",1)
161 cmd.set("field_of_view",20)
162 cmd.rock(0)
163 cmd.mset()
164 cmd.mstop()
169 cmd.set("suspend_updates",1,quiet=1)
170 cmd.disable()
171 cmd.delete("pept")
172 cmd.delete("pept_dist")
173 cmd.load("$PYMOL_DATA/demo/pept.pdb")
174 cmd.show("sticks","(pept and not i;5:7)")
175 cmd.show("surface","(pept and i;5,6)")
176 cmd.show("mesh","(pept and i;1,11,12,13)")
177 cmd.show("spheres","(?pept & resi 2+12+9+4 &! name C+N+O+CA)")
178 cmd.show("dots","(i;8)")
179 cmd.dist("pept_dist","(pept and i;1&n;OD2)","(pept and i;13&n;OG1)")
180 cmd.set("dot_width","2");
182 cmd.set("suspend_updates",0,quiet=1)
184 cmd.delete("pept")
185 cmd.delete("pept_dist")
191 cmd.disable()
192 cmd.set("suspend_updates",1,quiet=1)
193 cmd.load("$PYMOL_DATA/demo/pept.pdb","rep1")
194 cmd.alter("rep1///1-5+8-13/","ss='S'")
195 cmd.cartoon("auto")
196 cmd.hide("everything","rep1")
198 cmd.create("rep%d"%a,"rep1")
200 cmd.show(x, "rep%d" % y)
201 cmd.reset()
202 cmd.zoom("rep1",24)
211 cmd.set("suspend_updates",0,quiet=1)
214 cmd.set("suspend_updates",0,quiet=1)
215 cmd.refresh()
216 cmd.set("suspend_updates",1,quiet=1)
220 cmd.translate([xt*scale,yt*scale,0],object="rep%d"%a,camera=0)
225 cmd.translate([xt*scale,yt*scale,0],object="rep%d"%a,camera=0)
228 cmd.origin("rep%d"%a,object="rep%d"%a)
229 cmd.mset("1")
232 cmd.mdo(1,st)
233 cmd.set("suspend_updates",0,quiet=1)
234 cmd.mplay()
241 ext = cmd.get_extent("rep%d"%c)
248 cmd.set("cgo_line_width",1.5)
249 cmd.set("auto_zoom",0)
250 cmd.load_cgo(cgo,'reps')
251 cmd.set("auto_zoom",1)
253 cmd.delete("rep*")
254 cmd.mset()
255 cmd.mstop()
262 cmd.load("$PYMOL_DATA/demo/il2.pdb")
263 cmd.remove("hydro")
264 cmd.disable()
265 cmd.enable("il2")
266 cmd.set("ribbon_color","blue","il2")
267 cmd.set("roving_detail",1)
268 cmd.set("roving_origin",1)
269 cmd.set("stick_radius",0.12,"il2")
272 cmd.set_view ((\
280 cmd.delete("il2")
281 cmd.set("roving_detail",0)
282 cmd.refresh()
283 cmd.delete("rov_*")
288 cmd.load("$PYMOL_DATA/demo/il2.pdb")
289 cmd.set("suspend_updates",1,quiet=1)
290 cmd.remove("hydro")
291 cmd.disable()
292 cmd.enable("il2")
293 cmd.map_new("map","gaussian","0.75","il2")
294 cmd.feedback("disable","objectmesh","actions")
295 cmd.set("ribbon_color","purple","il2")
296 cmd.set("roving_detail",1)
297 cmd.set("roving_origin",1)
298 cmd.set("stick_radius",0.12,"il2")
299 cmd.set("roving_sticks",0)
300 cmd.set("roving_polar_contacts",0)
301 cmd.set("line_width","3")
302 cmd.set("roving_map1_name","map")
303 cmd.isomesh("rov_m1","map",9999.0,"il2")
304 cmd.color("density","rov_m1")
306 cmd.set_view ((\
314 cmd.set("suspend_updates",0,quiet=1)
315 cmd.refresh()
317 cmd.set("roving_detail",0)
318 cmd.set("roving_map1_name","")
319 cmd.set("roving_polar_contacts",7)
320 cmd.set("roving_sticks",6)
321 cmd.delete("il2")
322 cmd.delete("map")
323 cmd.set("line_width",1.5)
324 cmd.refresh()
325 cmd.set("roving_detail",0)
326 cmd.delete("rov_*")
327 cmd.sync()
332 cmd.set("suspend_updates",1,quiet=1)
333 cmd.disable()
334 cmd.delete("1tii")
335 cmd.load("$PYMOL_DATA/demo/1tii.pdb")
336 cmd.hide("(1tii)")
337 cmd.show("cartoon","1tii")
338 cmd.zoom("1tii")
339 cmd.spectrum("count","rainbow","1tii////ca")
340 cmd.set("cartoon_highlight_color","grey50","1tii")
341 cmd.set("cartoon_fancy_helices",1,"1tii")
343 cmd.set("suspend_updates",0,quiet=1)
344 cmd.refresh()
346 cmd.delete("1tii")
350 cmd.disable()
351 cmd.delete("pept")
352 cmd.delete("e_pot")
353 cmd.delete("e_lvl")
354 cmd.load("$PYMOL_DATA/demo/pept.pkl")
355 cmd.hide("(pept)")
356 cmd.show("surface","pept")
357 cmd.set("coulomb_dielectric",80.0)
358 cmd.map_new("e_pot","coulomb",1.0,"pept",5)
359 cmd.ramp_new("e_lvl","e_pot",[-3.6,-1.6,0.4])
360 cmd.set("surface_color","e_lvl","pept")
361 cmd.refresh()
363 cmd.delete("pept")
364 cmd.delete("e_pot")
365 cmd.delete("e_lvl")
370 cmd.set("suspend_updates",1,quiet=1)
371 cmd.disable()
372 cmd.delete("trans")
373 cmd.load("$PYMOL_DATA/demo/pept.pdb","trans")
374 cmd.hide("(trans)")
375 cmd.show("surface","trans")
376 cmd.show("sticks","trans")
377 cmd.set("surface_color","white","trans")
378 cmd.set("transparency",0.5,"trans")
379 cmd.zoom("trans")
381 cmd.set("suspend_updates",0,quiet=1)
382 cmd.refresh()
384 cmd.delete("trans")
388 cmd.set("suspend_updates",1,quiet=1)
389 cmd.disable()
390 cmd.delete("ray")
391 cmd.set("sphere_mode",5)
392 cmd.set("sphere_scale",1.0)
393 cmd.load("$PYMOL_DATA/demo/il2.pdb","ray")
394 cmd.remove("(ray and hydro)")
395 cmd.hide("lines","ray")
396 cmd.show("spheres","ray")
397 cmd.orient("ray")
398 cmd.turn("x",90)
400 cmd.mstop()
401 cmd.rock(0)
402 cmd.set("suspend_updates",0,quiet=1)
403 cmd.refresh()
404 cmd.do("ray")
406 cmd.delete("ray")
409 cmd.do("_ wizard")
413 cmd.set("suspend_updates",1,quiet=1)
414 cmd.disable()
415 cmd.delete("sculpt")
416 cmd.set("sphere_scale","1.0")
417 cmd.set("sphere_mode",5)
418 cmd.load("$PYMOL_DATA/demo/pept.pdb","sculpt")
419 cmd.hide("lines","sculpt")
421 cmd.show("spheres","sculpt")
424 cmd.frame(1)
425 cmd.set("auto_sculpt",1)
426 cmd.set("sculpting",1)
427 cmd.sculpt_activate("sculpt")
428 cmd.set("sculpting_cycles","100")
429 cmd.do("edit_mode")
430 cmd.set("valence","0.05")
431 cmd.set("suspend_updates",0,quiet=0)
432 cmd.sculpt_iterate("sculpt")
433 cmd.alter_state(1,"sculpt","x=x*1.5;y=y*0.1;z=z*1.5")
434 cmd.zoom()
436 cmd.unpick()
438 cmd.set("valence","0")
439 cmd.set("sculpting",0)
440 cmd.set("auto_sculpt",0)
441 cmd.delete("sculpt")
442 cmd.mouse()
447 cmd.set_wizard(pymol.wizard.stereodemo)
448 cmd.stereo("on")
449 cmd.set("max_threads",4)