Lines Matching refs:cmd
2 from pymol import cmd
12 def __init__(self,name=None,_self=cmd):
64 def __init__(self,_self=cmd):
65 self.cmd=_self
81 self.cmd.set("suspend_updates",1,quiet=1)
82 self.cmd.disable()
83 self.cmd.delete("pept")
84 self.cmd.delete("pept_dist")
85 self.cmd.load("$PYMOL_DATA/demo/pept.pdb")
86 self.cmd.hide("everything", "pept")
87 self.cmd.show("sticks","(pept and not i;5:7)")
88 self.cmd.show("surface","(pept and i;5,6)")
89 self.cmd.show("mesh","(pept and i;1,11,12,13)")
90 self.cmd.show("spheres","(?pept & resi 2+12+9+4 &! name C+N+O+CA)")
91 self.cmd.show("dots","(i;8)")
92 self.cmd.dist("pept_dist","(pept and i;1&n;OD2)","(pept and i;13&n;OG1)")
93 self.cmd.set("dot_width","2");
95 self.cmd.set("suspend_updates",0,quiet=1)
97 self.cmd.delete("pept")
98 self.cmd.delete("pept_dist")
104 self.cmd.disable()
105 self.cmd.set("suspend_updates",1,quiet=1)
106 self.cmd.mset()
107 self.cmd.set("movie_panel", 0)
108 self.cmd.load("$PYMOL_DATA/demo/pept.pdb","rep1")
109 self.cmd.alter("rep1///1-5+8-13/","ss='S'")
110 self.cmd.cartoon("auto")
111 self.cmd.hide("everything","rep1")
113 self.cmd.create("rep%d"%a,"rep1")
115 self.cmd.show(x, "rep%d" % y)
116 self.cmd.reset()
117 self.cmd.zoom("rep1",24)
118 util.cbay("rep2",_self=self.cmd)
119 util.cbac("rep3",_self=self.cmd)
120 util.cbas("rep4",_self=self.cmd)
121 util.cbab("rep5",_self=self.cmd)
122 util.cbaw("rep6",_self=self.cmd)
123 util.cbay("rep8",_self=self.cmd)
126 self.cmd.set("suspend_updates",0,quiet=1)
129 self.cmd.set("suspend_updates",0,quiet=1)
130 self.cmd.refresh()
131 self.cmd.set("suspend_updates",1,quiet=1)
135 self.cmd.translate([xt*scale,yt*scale,0],object="rep%d"%a,camera=0)
140 self.cmd.translate([xt*scale,yt*scale,0],object="rep%d"%a,camera=0)
143 self.cmd.origin("rep%d"%a,object="rep%d"%a)
144 self.cmd.mset("1")
146 self.cmd.mdo(1,st)
147 self.cmd.set("suspend_updates",0,quiet=1)
148 self.cmd.mplay()
155 ext = self.cmd.get_extent("rep%d"%c)
162 self.cmd.set("cgo_line_width",1.5)
163 self.cmd.set("auto_zoom",0)
164 self.cmd.load_cgo(cgo,'reps')
165 self.cmd.set("auto_zoom",1)
167 self.cmd.delete("rep*")
168 self.cmd.mset()
169 self.cmd.mstop()
170 self.cmd.set("movie_panel",1)
176 self.cmd.disable()
178 self.cmd.set_view( (\
185 self.cmd.load("$PYMOL_DATA/demo/1hpv.r3d","cgo1")
186 self.cmd.zoom("cgo1")
188 self.cmd.delete("cgo1")
192 self.cmd.disable()
194 self.cmd.set("suspend_updates",1,quiet=1)
195 self.cmd.do("run $PYMOL_DATA/demo/cgo03.py")
197 self.cmd.set("suspend_updates",0,quiet=1)
199 self.cmd.delete("cgo03")
200 self.cmd.mset()
201 self.cmd.mstop()
202 self.cmd.rewind()
206 self.cmd.disable()
207 self.cmd.delete("arg")
208 self.cmd.fragment("arg")
209 self.cmd.zoom("arg",2)
210 self.cmd.show("sticks","arg")
211 self.cmd.feedback('dis','sel','res')
214 self.cmd.set("suspend_updates",1,quiet=1)
215 self.cmd.edit("(arg & name CD)","(arg & name CG)",quiet=1)
216 self.cmd.torsion("6")
217 self.cmd.unpick()
218 self.cmd.edit("(arg & name CB)","(arg & name CA)",quiet=1)
219 self.cmd.torsion("2")
220 self.cmd.unpick()
222 self.cmd.set("suspend_updates",0,quiet=1)
223 self.cmd.refresh()
224 self.cmd.feedback('ena','sel','res')
226 self.cmd.delete("arg")
231 self.cmd.set("suspend_updates",1,quiet=1)
232 self.cmd.disable()
233 self.cmd.load("$TUT/1hpv.pdb")
234 util.chainbow("1hpv",_self=self.cmd)
235 self.cmd.hide("everything","1hpv")
236 self.cmd.show("cartoon","1hpv")
237 self.cmd.show("sticks","1hpv///200/")
238 self.cmd.create("1hpv_a","1hpv//A//")
239 self.cmd.set("cartoon_smooth_loops",0,"1hpv_a")
240 self.cmd.create("1hpv_b","1hpv//B//")
241 self.cmd.set("cartoon_smooth_loops",0,"1hpv_b")
242 self.cmd.create("1hpv_l","1hpv///200/")
243 util.cbay("1hpv_l",_self=self.cmd)
244 self.cmd.delete("1hpv")
245 self.cmd.set_view ((\
252 self.cmd.translate([-20,0,0],object="1hpv_a")
253 self.cmd.translate([20,0,0],object="1hpv_b")
254 self.cmd.zoom("center",30)
255 self.cmd.translate([0,10,00],object="1hpv_l")
257 self.cmd.set("suspend_updates",0,quiet=1)
258 self.cmd.refresh()
261 self.cmd.set("suspend_updates",1,quiet=1)
262 self.cmd.translate([1,0,0],object="1hpv_a")
263 self.cmd.translate([-1,0,0],object="1hpv_b")
264 self.cmd.translate([0,-0.5,0],object="1hpv_l")
266 self.cmd.set("suspend_updates",0,quiet=1)
267 self.cmd.refresh()
269 self.cmd.turn("y",6)
270 self.cmd.move('z',2)
271 self.cmd.move('y',-0.12)
272 self.cmd.refresh()
275 self.cmd.delete("1hpv_*")
280 self.cmd.set("suspend_updates",1,quiet=1)
281 self.cmd.load("$PYMOL_DATA/demo/il2.pdb")
282 self.cmd.hide("everything", "il2")
283 self.cmd.remove("hydro")
284 self.cmd.disable()
285 self.cmd.enable("il2")
286 self.cmd.set("ribbon_color","blue","il2")
287 self.cmd.set("roving_detail",1)
288 self.cmd.set("roving_origin",1)
289 self.cmd.set("stick_radius",0.12,"il2")
292 self.cmd.set_view ((\
300 self.cmd.set("suspend_updates", 0)
301 self.cmd.refresh()
303 self.cmd.delete("il2")
304 self.cmd.set("roving_detail",0)
305 self.cmd.refresh()
306 self.cmd.delete("rov_*")
311 self.cmd.set("suspend_updates",1,quiet=1)
312 self.cmd.load("$PYMOL_DATA/demo/il2.pdb")
313 self.cmd.hide("everything", "il2")
314 self.cmd.remove("hydro")
315 self.cmd.disable()
316 self.cmd.enable("il2")
317 self.cmd.map_new("map","gaussian","0.75","il2")
318 self.cmd.set("ribbon_color","purple","il2")
319 self.cmd.set("roving_detail",1)
320 self.cmd.set("roving_origin",1)
321 self.cmd.set("stick_radius",0.12,"il2")
322 self.cmd.set("roving_sticks",0)
323 self.cmd.set("roving_polar_contacts",0)
324 self.cmd.set("line_width","3")
325 self.cmd.set("roving_map1_name","map")
326 self.cmd.isomesh("rov_m1","map",9999.0,"il2")
327 self.cmd.color("density","rov_m1")
329 self.cmd.set_view ((\
337 self.cmd.set("suspend_updates",0,quiet=1)
338 self.cmd.refresh()
340 self.cmd.set("roving_detail",0)
341 self.cmd.set("roving_map1_name","")
342 self.cmd.set("roving_polar_contacts",7)
343 self.cmd.set("roving_sticks",6)
344 self.cmd.delete("il2")
345 self.cmd.delete("map")
346 self.cmd.set("line_width",1.5)
347 self.cmd.refresh()
348 self.cmd.set("roving_detail",0)
349 self.cmd.delete("rov_*")
350 self.cmd.sync()
355 self.cmd.set("suspend_updates",1,quiet=1)
356 self.cmd.disable()
357 self.cmd.delete("1tii")
358 self.cmd.load("$PYMOL_DATA/demo/1tii.pdb")
359 self.cmd.hide("(1tii)")
360 self.cmd.show("cartoon","1tii")
361 self.cmd.zoom("1tii")
362 self.cmd.spectrum("count","rainbow","1tii////CA")
363 self.cmd.set("cartoon_highlight_color","grey50","1tii")
364 self.cmd.set("cartoon_fancy_helices",1,"1tii")
366 self.cmd.set("suspend_updates",0,quiet=1)
367 self.cmd.refresh()
369 self.cmd.delete("1tii")
373 self.cmd.config_mouse('three_button_viewing')
374 self.cmd.disable()
375 self.cmd.delete("pept")
376 self.cmd.delete("e_pot")
377 self.cmd.delete("e_lvl")
378 self.cmd.load("$PYMOL_DATA/demo/pept.pkl")
379 self.cmd.hide("(pept)")
380 self.cmd.show("surface","pept")
381 self.cmd.set("coulomb_dielectric",80.0)
382 self.cmd.map_new("e_pot","coulomb",1.0,"pept",5)
383 self.cmd.ramp_new("e_lvl","e_pot",[-3.6,-1.6,0.4])
384 self.cmd.set("surface_color","e_lvl","pept")
385 self.cmd.refresh()
387 self.cmd.delete("pept")
388 self.cmd.delete("e_pot")
389 self.cmd.delete("e_lvl")
394 self.cmd.set("suspend_updates",1,quiet=1)
395 self.cmd.disable()
396 self.cmd.delete("trans")
397 self.cmd.load("$PYMOL_DATA/demo/pept.pdb","trans")
398 self.cmd.hide("(trans)")
399 self.cmd.show("surface","trans")
400 self.cmd.show("sticks","trans")
401 self.cmd.set("surface_color","white","trans")
402 self.cmd.set("transparency",0.5,"trans")
403 self.cmd.zoom("trans")
405 self.cmd.set("suspend_updates",0,quiet=1)
406 self.cmd.refresh()
408 self.cmd.delete("trans")
412 self.cmd.set("suspend_updates",1,quiet=1)
413 self.cmd.disable()
414 self.cmd.delete("ray")
415 self.cmd.load("$PYMOL_DATA/demo/il2.pdb","ray")
416 self.cmd.remove("(ray and hydro)")
417 self.cmd.hide("everything","ray")
418 self.cmd.show("spheres","ray")
419 self.cmd.orient("ray")
420 self.cmd.turn("x",90)
421 util.ray_shadows('heavy',_self=self.cmd)
422 self.cmd.set("suspend_updates",0,quiet=1)
423 self.cmd.refresh()
424 self.cmd.do("ray")
426 self.cmd.delete("ray")
429 self.cmd.do("_ wizard")
433 self.cmd.set("suspend_updates",1,quiet=1)
434 self.cmd.disable()
435 self.cmd.delete("sculpt")
436 self.cmd.load("$PYMOL_DATA/demo/pept.pdb","sculpt")
437 self.cmd.hide("everything","sculpt")
438 self.cmd.show("sticks","sculpt")
439 if self.cmd.get_setting_boolean("use_shaders"):
440 self.cmd.show("spheres","sculpt")
441 self.cmd.set("sphere_transparency","0.75","sculpt")
442 self.cmd.set("sphere_color","grey","sculpt")
443 self.cmd.frame(1)
444 self.cmd.set("auto_sculpt",1)
445 self.cmd.set("sculpting",1)
446 self.cmd.sculpt_activate("sculpt")
447 self.cmd.do("edit_mode")
448 self.cmd.set("valence","0.05")
449 self.cmd.set("suspend_updates",0,quiet=0)
450 self.cmd.unpick()
452 self.cmd.set("valence","0")
453 self.cmd.set("sculpting",0)
454 self.cmd.set("auto_sculpt",0)
455 self.cmd.delete("sculpt")
456 self.cmd.mouse()