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I'll be posting some ideas for logos and graphics for this page in the next week or so. | I'll be posting some ideas for logos and graphics for this page in the next week or so. | ||
| − | < | + | [[Image:Pymolwiki.png|PyMOL Wiki title image 1]] |
| + | |||
| + | == Code Test == | ||
| + | |||
| + | <source lang="python"> | ||
from math import log | from math import log | ||
base = 'expt100000.1HJM_int' | base = 'expt100000.1HJM_int' | ||
| Line 14: | Line 18: | ||
cmd.set('hash_max', 240) | cmd.set('hash_max', 240) | ||
repeat = 8 #number of frames to repeat each structure | repeat = 8 #number of frames to repeat each structure | ||
| − | + | ||
for n in range(1,501): | for n in range(1,501): | ||
curmol = base[0:5]+str(n).zfill(5)+base[10:] | curmol = base[0:5]+str(n).zfill(5)+base[10:] | ||
| + | # print curmol+'.pdb' | ||
cmd.load(curmol+'.pdb') | cmd.load(curmol+'.pdb') | ||
if n > 1: | if n > 1: | ||
cmd.fit(curmol+' and name ca and (resi 56 or resi 57 or resi 58)', oldmol+' and name ca and (resi 56 or resi 57 or resi 58)') | cmd.fit(curmol+' and name ca and (resi 56 or resi 57 or resi 58)', oldmol+' and name ca and (resi 56 or resi 57 or resi 58)') | ||
cmd.delete(oldmol) | cmd.delete(oldmol) | ||
| + | # cmd.reset(curmol+' and name ca and (resi 56 or resi 57 or resi 58)') | ||
| + | # cmd.origin(curmol+' and name ca and (resi 56 or resi 57 or resi 58)') | ||
| + | # cmd.zoom(curmol) | ||
else: | else: | ||
cmd.orient(curmol+' and name ca and (resi 56 or resi 57 or resi 58)') | cmd.orient(curmol+' and name ca and (resi 56 or resi 57 or resi 58)') | ||
cmd.center(curmol+' and name ca and (resi 56 or resi 57 or resi 58)') | cmd.center(curmol+' and name ca and (resi 56 or resi 57 or resi 58)') | ||
| + | # cmd.zoom(curmol) | ||
| + | # util.chainbow(curmol) | ||
cmd.spectrum('count', 'blue_white_red', '('+curmol+')',minimum=None, maximum=None, byres=1, quiet=1) | cmd.spectrum('count', 'blue_white_red', '('+curmol+')',minimum=None, maximum=None, byres=1, quiet=1) | ||
cmd.hide("lines", curmol) | cmd.hide("lines", curmol) | ||
# cmd.show("surface", curmol) | # cmd.show("surface", curmol) | ||
cmd.show("cartoon", curmol) | cmd.show("cartoon", curmol) | ||
| + | # cmd.set_view ('\ | ||
| + | # 1.000000000, 0.000000000, 0.000000000,\ | ||
| + | # 0.000000000, 1.000000000, 0.000000000,\ | ||
| + | # 0.000000000, 0.000000000, 1.000000000,\ | ||
| + | # 0.000000000, 0.000000000, -717.288574219,\ | ||
| + | # 35.836936951, 12.674762726, -6.756893158,\ | ||
| + | # 565.515808105, 869.061340332, 0.000000000' ) | ||
cmd.set_view('\ | cmd.set_view('\ | ||
1.000000000, 0.000000000, 0.000000000,\ | 1.000000000, 0.000000000, 0.000000000,\ | ||
| Line 36: | Line 53: | ||
205.446594238, 263.989440918, 0.000000000' ) | 205.446594238, 263.989440918, 0.000000000' ) | ||
cmd.translate([0,0,-0.0008*n*log(n)], curmol, 0, 1, None) | cmd.translate([0,0,-0.0008*n*log(n)], curmol, 0, 1, None) | ||
| + | # cmd.zoom(curmol) | ||
cmd.clip('far', -0.5*n*log(n)) | cmd.clip('far', -0.5*n*log(n)) | ||
cmd.clip('near', -0.05*n*log(n)) | cmd.clip('near', -0.05*n*log(n)) | ||
## Uncomment one line to render frames ## | ## Uncomment one line to render frames ## | ||
| − | # cmd.ray(1680, 1050) # 16:10 1764000 | + | # cmd.ray(1680, 1050) # 16:10 1764000 |
# cmd.ray(1024, 576) # 16:9 589824 | # cmd.ray(1024, 576) # 16:9 589824 | ||
# cmd.ray(800, 450) # 16:9 360000 | # cmd.ray(800, 450) # 16:9 360000 | ||
# cmd.ray(640, 360) # 16:9 230400 | # cmd.ray(640, 360) # 16:9 230400 | ||
# cmd.ray(480, 270) # 16:9 129600 | # cmd.ray(480, 270) # 16:9 129600 | ||
| − | # cmd.ray(240, 180) # 16:9 43200 | + | # cmd.ray(240, 180) # 16:9 43200 |
# cmd.ray(1024, 768) # 4:3 786432 | # cmd.ray(1024, 768) # 4:3 786432 | ||
| − | + | cmd.ray(800, 600) # 4:3 4800000 | |
# cmd.ray(640, 480) # 4:3 307200 | # cmd.ray(640, 480) # 4:3 307200 | ||
# cmd.ray(480, 360) # 4:3 172800 | # cmd.ray(480, 360) # 4:3 172800 | ||
# cmd.ray(240, 180) # 4:3 43200 | # cmd.ray(240, 180) # 4:3 43200 | ||
## Uncomment loop to repeat frames ## | ## Uncomment loop to repeat frames ## | ||
| − | + | for i in range(0,repeat): | |
| − | + | cmd.png("imgs/"+str((n-1) * repeat + i).zfill(5)+".png") | |
cmd.refresh() | cmd.refresh() | ||
oldmol = curmol | oldmol = curmol | ||
| − | </ | + | |
| + | </source> | ||
Latest revision as of 01:42, 28 March 2014
Tzintzuni Garcia
University of Texas Medical Branch Department of Human Biological Chemistry and Genetics Graduate Student
Graphics
I'll be posting some ideas for logos and graphics for this page in the next week or so.
Code Test
from math import log
base = 'expt100000.1HJM_int'
cmd.set('auto_zoom', 'off')
cmd.set('bg_rgb', ('0', '0', '0'))
cmd.set('hash_max', 240)
repeat = 8 #number of frames to repeat each structure
for n in range(1,501):
curmol = base[0:5]+str(n).zfill(5)+base[10:]
# print curmol+'.pdb'
cmd.load(curmol+'.pdb')
if n > 1:
cmd.fit(curmol+' and name ca and (resi 56 or resi 57 or resi 58)', oldmol+' and name ca and (resi 56 or resi 57 or resi 58)')
cmd.delete(oldmol)
# cmd.reset(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')
# cmd.origin(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')
# cmd.zoom(curmol)
else:
cmd.orient(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')
cmd.center(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')
# cmd.zoom(curmol)
# util.chainbow(curmol)
cmd.spectrum('count', 'blue_white_red', '('+curmol+')',minimum=None, maximum=None, byres=1, quiet=1)
cmd.hide("lines", curmol)
# cmd.show("surface", curmol)
cmd.show("cartoon", curmol)
# cmd.set_view ('\
# 1.000000000, 0.000000000, 0.000000000,\
# 0.000000000, 1.000000000, 0.000000000,\
# 0.000000000, 0.000000000, 1.000000000,\
# 0.000000000, 0.000000000, -717.288574219,\
# 35.836936951, 12.674762726, -6.756893158,\
# 565.515808105, 869.061340332, 0.000000000' )
cmd.set_view('\
1.000000000, 0.000000000, 0.000000000,\
0.000000000, 1.000000000, 0.000000000,\
0.000000000, 0.000000000, 1.000000000,\
0.000000000, 0.000000000, -234.718002319,\
10.384142876, 15.351722717, 11.246277809,\
205.446594238, 263.989440918, 0.000000000' )
cmd.translate([0,0,-0.0008*n*log(n)], curmol, 0, 1, None)
# cmd.zoom(curmol)
cmd.clip('far', -0.5*n*log(n))
cmd.clip('near', -0.05*n*log(n))
## Uncomment one line to render frames ##
# cmd.ray(1680, 1050) # 16:10 1764000
# cmd.ray(1024, 576) # 16:9 589824
# cmd.ray(800, 450) # 16:9 360000
# cmd.ray(640, 360) # 16:9 230400
# cmd.ray(480, 270) # 16:9 129600
# cmd.ray(240, 180) # 16:9 43200
# cmd.ray(1024, 768) # 4:3 786432
cmd.ray(800, 600) # 4:3 4800000
# cmd.ray(640, 480) # 4:3 307200
# cmd.ray(480, 360) # 4:3 172800
# cmd.ray(240, 180) # 4:3 43200
## Uncomment loop to repeat frames ##
for i in range(0,repeat):
cmd.png("imgs/"+str((n-1) * repeat + i).zfill(5)+".png")
cmd.refresh()
oldmol = curmol