Category:Discussion: Difference between revisions

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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:
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. 
<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 22:06, 19 February 2005

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