User:Orpheus: Difference between revisions

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== Graphics ==
== Graphics ==
I'll be posting some ideas for logos and graphics for this page in the next week or so.
I'll be posting some ideas for logos and graphics for this page in the next week or so.
<code>
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
</code>

Revision as of 19:13, 17 February 2005

Tzintzuni Garcia

University of Texas Medical Branch
Department of Human Biological Chemistry and Genetics
Graduate Student

Graphics

I'll be posting some ideas for logos and graphics for this page in the next week or so.

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