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== Code Display Conventions ==
 
== Code Display Conventions ==
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This is an experiment in displaying source code:
 
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I found this great open source syntax highlighter written in PHP.  You can see this code highlighted [http://qbnz.com/highlighter/demo.php?id=6350&lang=python here] for the next 7 days. 
 
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<pre>
 
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from math import log
 
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base = 'expt100000.1HJM_int'
 
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cmd.set('auto_zoom', 'off')
 
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cmd.set('bg_rgb', ('0', '0', '0'))
 
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cmd.set('hash_max', 240)
 
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repeat = 8 #number of frames to repeat each structure
 
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for n in range(1,501):
 
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    curmol = base[0:5]+str(n).zfill(5)+base[10:]
 
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    cmd.load(curmol+'.pdb')
 
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    if n > 1:
 
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        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)')
 
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        cmd.delete(oldmol)
 
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    else:
 
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        cmd.orient(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')
 
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        cmd.center(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')
 
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    cmd.spectrum('count', 'blue_white_red', '('+curmol+')',minimum=None, maximum=None, byres=1, quiet=1)
 
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    cmd.hide("lines", curmol)
 
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#    cmd.show("surface", curmol)
 
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    cmd.show("cartoon", curmol)
 
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    cmd.set_view('\
 
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    1.000000000,    0.000000000,    0.000000000,\
 
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    0.000000000,    1.000000000,    0.000000000,\
 
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    0.000000000,    0.000000000,    1.000000000,\
 
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    0.000000000,    0.000000000, -234.718002319,\
 
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    10.384142876,  15.351722717,  11.246277809,\
 
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  205.446594238,  263.989440918,    0.000000000' )
 
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    cmd.translate([0,0,-0.0008*n*log(n)], curmol, 0, 1, None)
 
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    cmd.clip('far', -0.5*n*log(n))
 
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    cmd.clip('near', -0.05*n*log(n))
 
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## Uncomment one line to render frames ##
 
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#    cmd.ray(1680, 1050) # 16:10 1764000
 
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#    cmd.ray(1024, 576) # 16:9 589824
 
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#    cmd.ray(800, 450) # 16:9 360000
 
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#    cmd.ray(640, 360) # 16:9 230400
 
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#    cmd.ray(480, 270) # 16:9 129600
 
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#    cmd.ray(240, 180) # 16:9 43200
 
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#    cmd.ray(1024, 768) # 4:3 786432
 
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#    cmd.ray(800, 600) # 4:3 4800000
 
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#    cmd.ray(640, 480) # 4:3 307200
 
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#    cmd.ray(480, 360) # 4:3 172800
 
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#    cmd.ray(240, 180) # 4:3 43200
 
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## Uncomment loop to repeat frames ##
 
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#    for i in range(0,repeat):
 
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#        cmd.png("imgs/"+str((n-1) * repeat + i).zfill(5)+".png")
 
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    cmd.refresh()
 
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    oldmol = curmol
 
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</pre>
 

Revision as of 20:38, 19 February 2005

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

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