User:Orpheus

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.

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)

1. 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))

1. 1. Uncomment one line to render frames ##
2. cmd.ray(1680, 1050) # 16:10 1764000
3. cmd.ray(1024, 576) # 16:9 589824
4. cmd.ray(800, 450) # 16:9 360000
5. cmd.ray(640, 360) # 16:9 230400
6. cmd.ray(480, 270) # 16:9 129600
7. cmd.ray(240, 180) # 16:9 43200
8. cmd.ray(1024, 768) # 4:3 786432
9. cmd.ray(800, 600) # 4:3 4800000
10. cmd.ray(640, 480) # 4:3 307200
11. cmd.ray(480, 360) # 4:3 172800
12. cmd.ray(240, 180) # 4:3 43200
    1. Uncomment loop to repeat frames ##
13. for i in range(0,repeat):
14. cmd.png("imgs/"+str((n-1) * repeat + i).zfill(5)+".png")

   cmd.refresh()
   oldmol = curmol