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

Latest revision as of 01:29, 28 March 2014

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