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== Expanded Schema ==
 
Proposal to incorporate more than just a manual into this site:
 
  
# Manual
 
## GUI
 
## Command Script
 
## Python API
 
## Settings
 
## Miscellaneous
 
## Command Line
 
# Meta Manual
 
## Selections
 
## Colors
 
## Palettes
 
## Writing/Running Scripts
 
## Customizing PyMOL
 
# Discussions
 
## News
 
## Development
 
## Questions
 
# Special Topics
 
## Movies and Animation
 
## biochemical calculations
 
## NMR
 
## Crystallography
 
## DNA
 
## Stereo 3D
 
 
== Code Display Conventions ==
 
This is an experiment in displaying source code:
 
<pre>
 
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
 
</pre>
 

Latest revision as of 01:29, 28 March 2014

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