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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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|
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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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|
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| == Code Display Conventions ==
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| This is an experiment in displaying source code:
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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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|
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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>
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