Category:Discussion

Expanded Schema

Proposal to incorporate more than just a manual into this site:

1. Manual
   1. GUI
   2. Command Script
   3. Python API
   4. Settings
   5. Miscellaneous
   6. Command Line
2. Meta Manual
   1. Selections
   2. Colors
   3. Palettes
   4. Writing/Running Scripts
   5. Customizing PyMOL
3. Discussions
   1. News
   2. Development
   3. Questions
4. Special Topics
   1. Movies and Animation
   2. biochemical calculations
   3. NMR
   4. Crystallography
   5. DNA
   6. Stereo 3D

Code Display Conventions

This is an experiment in displaying source code: I found this great open source syntax highlighter written in PHP. You can see this code highlighted here for the next 7 days.

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:]
    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)
    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.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, -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.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