https://pymolwiki.org/api.php?action=feedcontributions&user=Orpheus&feedformat=atomPyMOLWiki - User contributions [en]2024-03-28T14:56:20ZUser contributionsMediaWiki 1.35.7https://pymolwiki.org/index.php?title=User:Orpheus&diff=2777User:Orpheus2005-02-19T22:08:42Z<p>Orpheus: /* Code Test */</p>
<hr />
<div>== Tzintzuni Garcia ==<br />
University of Texas Medical Branch<br />
Department of Human Biological Chemistry and Genetics<br />
Graduate Student<br />
<br />
== Graphics ==<br />
I'll be posting some ideas for logos and graphics for this page in the next week or so.<br />
<br />
[[Image:Pymolwiki.png|PyMOL Wiki title image 1]]<br />
<br />
== Code Test ==<br />
<br />
<source lang="python"><br />
from math import log<br />
base = 'expt100000.1HJM_int'<br />
cmd.set('auto_zoom', 'off')<br />
cmd.set('bg_rgb', ('0', '0', '0'))<br />
cmd.set('hash_max', 240)<br />
repeat = 8 #number of frames to repeat each structure<br />
<br />
for n in range(1,501):<br />
curmol = base[0:5]+str(n).zfill(5)+base[10:]<br />
# print curmol+'.pdb'<br />
cmd.load(curmol+'.pdb')<br />
if n > 1:<br />
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)')<br />
cmd.delete(oldmol)<br />
# cmd.reset(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')<br />
# cmd.origin(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')<br />
# cmd.zoom(curmol)<br />
else:<br />
cmd.orient(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')<br />
cmd.center(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')<br />
# cmd.zoom(curmol)<br />
# util.chainbow(curmol)<br />
cmd.spectrum('count', 'blue_white_red', '('+curmol+')',minimum=None, maximum=None, byres=1, quiet=1)<br />
cmd.hide("lines", curmol)<br />
# cmd.show("surface", curmol)<br />
cmd.show("cartoon", curmol)<br />
# cmd.set_view ('\<br />
# 1.000000000, 0.000000000, 0.000000000,\<br />
# 0.000000000, 1.000000000, 0.000000000,\<br />
# 0.000000000, 0.000000000, 1.000000000,\<br />
# 0.000000000, 0.000000000, -717.288574219,\<br />
# 35.836936951, 12.674762726, -6.756893158,\<br />
# 565.515808105, 869.061340332, 0.000000000' )<br />
cmd.set_view('\<br />
1.000000000, 0.000000000, 0.000000000,\<br />
0.000000000, 1.000000000, 0.000000000,\<br />
0.000000000, 0.000000000, 1.000000000,\<br />
0.000000000, 0.000000000, -234.718002319,\<br />
10.384142876, 15.351722717, 11.246277809,\<br />
205.446594238, 263.989440918, 0.000000000' )<br />
cmd.translate([0,0,-0.0008*n*log(n)], curmol, 0, 1, None)<br />
# cmd.zoom(curmol)<br />
cmd.clip('far', -0.5*n*log(n))<br />
cmd.clip('near', -0.05*n*log(n))<br />
## Uncomment one line to render frames ##<br />
# cmd.ray(1680, 1050) # 16:10 1764000 <br />
# cmd.ray(1024, 576) # 16:9 589824<br />
# cmd.ray(800, 450) # 16:9 360000<br />
# cmd.ray(640, 360) # 16:9 230400<br />
# cmd.ray(480, 270) # 16:9 129600<br />
# cmd.ray(240, 180) # 16:9 43200 <br />
# cmd.ray(1024, 768) # 4:3 786432<br />
cmd.ray(800, 600) # 4:3 4800000<br />
# cmd.ray(640, 480) # 4:3 307200<br />
# cmd.ray(480, 360) # 4:3 172800<br />
# cmd.ray(240, 180) # 4:3 43200<br />
## Uncomment loop to repeat frames ##<br />
for i in range(0,repeat):<br />
cmd.png("imgs/"+str((n-1) * repeat + i).zfill(5)+".png")<br />
cmd.refresh()<br />
oldmol = curmol<br />
<br />
</source></div>Orpheushttps://pymolwiki.org/index.php?title=User:Orpheus&diff=248User:Orpheus2005-02-19T22:06:46Z<p>Orpheus: /* Code Test */</p>
<hr />
<div>== Tzintzuni Garcia ==<br />
University of Texas Medical Branch<br />
Department of Human Biological Chemistry and Genetics<br />
Graduate Student<br />
<br />
== Graphics ==<br />
I'll be posting some ideas for logos and graphics for this page in the next week or so.<br />
<br />
[[Image:Pymolwiki.png|PyMOL Wiki title image 1]]<br />
<br />
== Code Test ==<br />
<br />
<source lang="python"><br />
from math import log<br />
base = 'expt100000.1HJM_int'<br />
cmd.set('auto_zoom', 'off')<br />
cmd.set('bg_rgb', ('0', '0', '0'))<br />
cmd.set('hash_max', 240)<br />
repeat = 8 #number of frames to repeat each structure<br />
<br />
for n in range(1,501):<br />
curmol = base[0:5]+str(n).zfill(5)+base[10:]<br />
# print curmol+'.pdb'<br />
cmd.load(curmol+'.pdb')<br />
if n > 1:<br />
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)')<br />
cmd.delete(oldmol)<br />
# cmd.reset(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')<br />
# cmd.origin(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')<br />
# cmd.zoom(curmol)<br />
else:<br />
cmd.orient(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')<br />
cmd.center(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')<br />
# cmd.zoom(curmol)<br />
# util.chainbow(curmol)<br />
cmd.spectrum('count', 'blue_white_red', '('+curmol+')',minimum=None, maximum=None, byres=1, quiet=1)<br />
cmd.hide("lines", curmol)<br />
# cmd.show("surface", curmol)<br />
cmd.show("cartoon", curmol)<br />
# cmd.set_view ('\<br />
# 1.000000000, 0.000000000, 0.000000000,\<br />
# 0.000000000, 1.000000000, 0.000000000,\<br />
# 0.000000000, 0.000000000, 1.000000000,\<br />
# 0.000000000, 0.000000000, -717.288574219,\<br />
# 35.836936951, 12.674762726, -6.756893158,\<br />
# 565.515808105, 869.061340332, 0.000000000' )<br />
cmd.set_view('\<br />
1.000000000, 0.000000000, 0.000000000,\<br />
0.000000000, 1.000000000, 0.000000000,\<br />
0.000000000, 0.000000000, 1.000000000,\<br />
0.000000000, 0.000000000, -234.718002319,\<br />
10.384142876, 15.351722717, 11.246277809,\<br />
205.446594238, 263.989440918, 0.000000000' )<br />
cmd.translate([0,0,-0.0008*n*log(n)], curmol, 0, 1, None)<br />
# cmd.zoom(curmol)<br />
cmd.clip('far', -0.5*n*log(n))<br />
cmd.clip('near', -0.05*n*log(n))<br />
## Uncomment one line to render frames ##<br />
# cmd.ray(1680, 1050) # 16:10 1764000 <br />
# cmd.ray(1024, 576) # 16:9 589824<br />
# cmd.ray(800, 450) # 16:9 360000<br />
# cmd.ray(640, 360) # 16:9 230400<br />
# cmd.ray(480, 270) # 16:9 129600<br />
# cmd.ray(240, 180) # 16:9 43200 <br />
# cmd.ray(1024, 768) # 4:3 786432<br />
cmd.ray(800, 600) # 4:3 4800000<br />
# cmd.ray(640, 480) # 4:3 307200<br />
# cmd.ray(480, 360) # 4:3 172800<br />
# cmd.ray(240, 180) # 4:3 43200<br />
## Uncomment loop to repeat frames ##<br />
for i in range(0,repeat):<br />
cmd.png("imgs/"+str((n-1) * repeat + i).zfill(5)+".png")<br />
cmd.refresh()<br />
oldmol = curmol<br />
<br />
</source></div>Orpheushttps://pymolwiki.org/index.php?title=User:Orpheus&diff=246User:Orpheus2005-02-19T22:05:19Z<p>Orpheus: /* Code Test */</p>
<hr />
<div>== Tzintzuni Garcia ==<br />
University of Texas Medical Branch<br />
Department of Human Biological Chemistry and Genetics<br />
Graduate Student<br />
<br />
== Graphics ==<br />
I'll be posting some ideas for logos and graphics for this page in the next week or so.<br />
<br />
[[Image:Pymolwiki.png|PyMOL Wiki title image 1]]<br />
<br />
== Code Test ==<br />
<br />
<source lang="python"><br />
from math import log<br />
base = 'expt100000.1HJM_int'<br />
cmd.set('auto_zoom', 'off')<br />
cmd.set('bg_rgb', ('0', '0', '0'))<br />
cmd.set('hash_max', 240)<br />
repeat = 8 #number of frames to repeat each structure<br />
<br />
for n in range(1,501):<br />
curmol = base[0:5]+str(n).zfill(5)+base[10:]<br />
# print curmol+'.pdb'<br />
cmd.load(curmol+'.pdb')<br />
if n > 1:<br />
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)')<br />
cmd.delete(oldmol)<br />
# cmd.reset(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')<br />
# cmd.origin(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')<br />
# cmd.zoom(curmol)<br />
else:<br />
cmd.orient(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')<br />
cmd.center(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')<br />
# cmd.zoom(curmol)<br />
# util.chainbow(curmol)<br />
cmd.spectrum('count', 'blue_white_red', '('+curmol+')',minimum=None, maximum=None, byres=1, quiet=1)<br />
cmd.hide("lines", curmol)<br />
# cmd.show("surface", curmol)<br />
cmd.show("cartoon", curmol)<br />
# cmd.set_view ('\<br />
# 1.000000000, 0.000000000, 0.000000000,\<br />
# 0.000000000, 1.000000000, 0.000000000,\<br />
# 0.000000000, 0.000000000, 1.000000000,\<br />
# 0.000000000, 0.000000000, -717.288574219,\<br />
# 35.836936951, 12.674762726, -6.756893158,\<br />
# 565.515808105, 869.061340332, 0.000000000' )<br />
cmd.set_view('\<br />
1.000000000, 0.000000000, 0.000000000,\<br />
0.000000000, 1.000000000, 0.000000000,\<br />
0.000000000, 0.000000000, 1.000000000,\<br />
0.000000000, 0.000000000, -234.718002319,\<br />
10.384142876, 15.351722717, 11.246277809,\<br />
205.446594238, 263.989440918, 0.000000000' )<br />
cmd.translate([0,0,-0.0008*n*log(n)], curmol, 0, 1, None)<br />
# cmd.zoom(curmol)<br />
cmd.clip('far', -0.5*n*log(n))<br />
cmd.clip('near', -0.05*n*log(n))<br />
## Uncomment one line to render frames ##<br />
# cmd.ray(1680, 1050) # 16:10 1764000 <br />
# cmd.ray(1024, 576) # 16:9 589824<br />
# cmd.ray(800, 450) # 16:9 360000<br />
# cmd.ray(640, 360) # 16:9 230400<br />
# cmd.ray(480, 270) # 16:9 129600<br />
# cmd.ray(240, 180) # 16:9 43200 <br />
# cmd.ray(1024, 768) # 4:3 786432<br />
cmd.ray(800, 600) # 4:3 4800000<br />
# cmd.ray(640, 480) # 4:3 307200<br />
# cmd.ray(480, 360) # 4:3 172800<br />
# cmd.ray(240, 180) # 4:3 43200<br />
## Uncomment loop to repeat frames ##<br />
for i in range(0,repeat):<br />
cmd.png("imgs/"+str((n-1) * repeat + i).zfill(5)+".png")<br />
cmd.refresh()<br />
oldmol = curmol<br />
<br />
</source></div>Orpheushttps://pymolwiki.org/index.php?title=User:Orpheus&diff=243User:Orpheus2005-02-19T22:03:46Z<p>Orpheus: /* Code Test */</p>
<hr />
<div>== Tzintzuni Garcia ==<br />
University of Texas Medical Branch<br />
Department of Human Biological Chemistry and Genetics<br />
Graduate Student<br />
<br />
== Graphics ==<br />
I'll be posting some ideas for logos and graphics for this page in the next week or so.<br />
<br />
[[Image:Pymolwiki.png|PyMOL Wiki title image 1]]<br />
<br />
== Code Test ==<br />
<br />
<source lang="python"><br />
from math import log<br />
base = 'expt100000.1HJM_int'<br />
cmd.set('auto_zoom', 'off')<br />
cmd.set('bg_rgb', ('0', '0', '0'))<br />
cmd.set('hash_max', 240)<br />
repeat = 8 #number of frames to repeat each structure<br />
<br />
for n in range(1,501):<br />
curmol = base[0:5]+str(n).zfill(5)+base[10:]<br />
# print curmol+'.pdb'<br />
cmd.load(curmol+'.pdb')<br />
if n > 1:<br />
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)')<br />
cmd.delete(oldmol)<br />
# cmd.reset(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')<br />
# cmd.origin(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')<br />
# cmd.zoom(curmol)<br />
else:<br />
cmd.orient(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')<br />
cmd.center(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')<br />
# cmd.zoom(curmol)<br />
# util.chainbow(curmol)<br />
cmd.spectrum('count', 'blue_white_red', '('+curmol+')',minimum=None, maximum=None, byres=1, quiet=1)<br />
cmd.hide("lines", curmol)<br />
# cmd.show("surface", curmol)<br />
cmd.show("cartoon", curmol)<br />
# cmd.set_view ('\<br />
# 1.000000000, 0.000000000, 0.000000000,\<br />
# 0.000000000, 1.000000000, 0.000000000,\<br />
# 0.000000000, 0.000000000, 1.000000000,\<br />
# 0.000000000, 0.000000000, -717.288574219,\<br />
# 35.836936951, 12.674762726, -6.756893158,\<br />
# 565.515808105, 869.061340332, 0.000000000' )<br />
cmd.set_view('\<br />
1.000000000, 0.000000000, 0.000000000,\<br />
0.000000000, 1.000000000, 0.000000000,\<br />
0.000000000, 0.000000000, 1.000000000,\<br />
0.000000000, 0.000000000, -234.718002319,\<br />
10.384142876, 15.351722717, 11.246277809,\<br />
205.446594238, 263.989440918, 0.000000000' )<br />
cmd.translate([0,0,-0.0008*n*log(n)], curmol, 0, 1, None)<br />
# cmd.zoom(curmol)<br />
cmd.clip('far', -0.5*n*log(n))<br />
cmd.clip('near', -0.05*n*log(n))<br />
## Uncomment one line to render frames ##<br />
# cmd.ray(1680, 1050) # 16:10 1764000 <br />
# cmd.ray(1024, 576) # 16:9 589824<br />
# cmd.ray(800, 450) # 16:9 360000<br />
# cmd.ray(640, 360) # 16:9 230400<br />
# cmd.ray(480, 270) # 16:9 129600<br />
# cmd.ray(240, 180) # 16:9 43200 <br />
# cmd.ray(1024, 768) # 4:3 786432<br />
cmd.ray(800, 600) # 4:3 4800000<br />
# cmd.ray(640, 480) # 4:3 307200<br />
# cmd.ray(480, 360) # 4:3 172800<br />
# cmd.ray(240, 180) # 4:3 43200<br />
## Uncomment loop to repeat frames ##<br />
for i in range(0,repeat):<br />
cmd.png("imgs/"+str((n-1) * repeat + i).zfill(5)+".png")<br />
cmd.refresh()<br />
oldmol = curmol<br />
<br />
</source></div>Orpheushttps://pymolwiki.org/index.php?title=User:Orpheus&diff=241User:Orpheus2005-02-19T22:02:29Z<p>Orpheus: /* Code Test */</p>
<hr />
<div>== Tzintzuni Garcia ==<br />
University of Texas Medical Branch<br />
Department of Human Biological Chemistry and Genetics<br />
Graduate Student<br />
<br />
== Graphics ==<br />
I'll be posting some ideas for logos and graphics for this page in the next week or so.<br />
<br />
[[Image:Pymolwiki.png|PyMOL Wiki title image 1]]<br />
<br />
== Code Test ==<br />
<br />
<source lang="python"><br />
from math import log<br />
base = 'expt100000.1HJM_int'<br />
cmd.set('auto_zoom', 'off')<br />
cmd.set('bg_rgb', ('0', '0', '0'))<br />
cmd.set('hash_max', 240)<br />
repeat = 8 #number of frames to repeat each structure<br />
<br />
for n in range(1,501):<br />
curmol = base[0:5]+str(n).zfill(5)+base[10:]<br />
# print curmol+'.pdb'<br />
cmd.load(curmol+'.pdb')<br />
if n > 1:<br />
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)')<br />
cmd.delete(oldmol)<br />
# cmd.reset(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')<br />
# cmd.origin(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')<br />
# cmd.zoom(curmol)<br />
else:<br />
cmd.orient(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')<br />
cmd.center(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')<br />
# cmd.zoom(curmol)<br />
# util.chainbow(curmol)<br />
cmd.spectrum('count', 'blue_white_red', '('+curmol+')',minimum=None, maximum=None, byres=1, quiet=1)<br />
cmd.hide("lines", curmol)<br />
# cmd.show("surface", curmol)<br />
cmd.show("cartoon", curmol)<br />
# cmd.set_view ('\<br />
# 1.000000000, 0.000000000, 0.000000000,\<br />
# 0.000000000, 1.000000000, 0.000000000,\<br />
# 0.000000000, 0.000000000, 1.000000000,\<br />
# 0.000000000, 0.000000000, -717.288574219,\<br />
# 35.836936951, 12.674762726, -6.756893158,\<br />
# 565.515808105, 869.061340332, 0.000000000' )<br />
cmd.set_view('\<br />
1.000000000, 0.000000000, 0.000000000,\<br />
0.000000000, 1.000000000, 0.000000000,\<br />
0.000000000, 0.000000000, 1.000000000,\<br />
0.000000000, 0.000000000, -234.718002319,\<br />
10.384142876, 15.351722717, 11.246277809,\<br />
205.446594238, 263.989440918, 0.000000000' )<br />
cmd.translate([0,0,-0.0008*n*log(n)], curmol, 0, 1, None)<br />
# cmd.zoom(curmol)<br />
cmd.clip('far', -0.5*n*log(n))<br />
cmd.clip('near', -0.05*n*log(n))<br />
## Uncomment one line to render frames ##<br />
# cmd.ray(1680, 1050) # 16:10 1764000 <br />
# cmd.ray(1024, 576) # 16:9 589824<br />
# cmd.ray(800, 450) # 16:9 360000<br />
# cmd.ray(640, 360) # 16:9 230400<br />
# cmd.ray(480, 270) # 16:9 129600<br />
# cmd.ray(240, 180) # 16:9 43200 <br />
# cmd.ray(1024, 768) # 4:3 786432<br />
cmd.ray(800, 600) # 4:3 4800000<br />
# cmd.ray(640, 480) # 4:3 307200<br />
# cmd.ray(480, 360) # 4:3 172800<br />
# cmd.ray(240, 180) # 4:3 43200<br />
## Uncomment loop to repeat frames ##<br />
for i in range(0,repeat):<br />
cmd.png("imgs/"+str((n-1) * repeat + i).zfill(5)+".png")<br />
cmd.refresh()<br />
oldmol = curmol<br />
<br />
</source></div>Orpheushttps://pymolwiki.org/index.php?title=User:Orpheus&diff=238User:Orpheus2005-02-19T21:58:22Z<p>Orpheus: </p>
<hr />
<div>== Tzintzuni Garcia ==<br />
University of Texas Medical Branch<br />
Department of Human Biological Chemistry and Genetics<br />
Graduate Student<br />
<br />
== Graphics ==<br />
I'll be posting some ideas for logos and graphics for this page in the next week or so.<br />
<br />
[[Image:Pymolwiki.png|PyMOL Wiki title image 1]]<br />
<br />
== Code Test ==<br />
<br />
<source lang="python"><br />
from math import log<br />
base = 'expt100000.1HJM_int'<br />
cmd.set('auto_zoom', 'off')<br />
cmd.set('bg_rgb', ('0', '0', '0'))<br />
cmd.set('hash_max', 240)<br />
repeat = 8 #number of frames to repeat each structure<br />
<br />
for n in range(1,501):<br />
curmol = base[0:5]+str(n).zfill(5)+base[10:]<br />
# print curmol+'.pdb'<br />
cmd.load(curmol+'.pdb')<br />
if n > 1:<br />
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)')<br />
cmd.delete(oldmol)<br />
# cmd.reset(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')<br />
# cmd.origin(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')<br />
# cmd.zoom(curmol)<br />
else:<br />
cmd.orient(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')<br />
cmd.center(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')<br />
# cmd.zoom(curmol)<br />
# util.chainbow(curmol)<br />
cmd.spectrum('count', 'blue_white_red', '('+curmol+')',minimum=None, maximum=None, byres=1, quiet=1)<br />
cmd.hide("lines", curmol)<br />
# cmd.show("surface", curmol)<br />
cmd.show("cartoon", curmol)<br />
# cmd.set_view ('\<br />
# 1.000000000, 0.000000000, 0.000000000,\<br />
# 0.000000000, 1.000000000, 0.000000000,\<br />
# 0.000000000, 0.000000000, 1.000000000,\<br />
# 0.000000000, 0.000000000, -717.288574219,\<br />
# 35.836936951, 12.674762726, -6.756893158,\<br />
# 565.515808105, 869.061340332, 0.000000000' )<br />
cmd.set_view('\<br />
1.000000000, 0.000000000, 0.000000000,\<br />
0.000000000, 1.000000000, 0.000000000,\<br />
0.000000000, 0.000000000, 1.000000000,\<br />
0.000000000, 0.000000000, -234.718002319,\<br />
10.384142876, 15.351722717, 11.246277809,\<br />
205.446594238, 263.989440918, 0.000000000' )<br />
cmd.translate([0,0,-0.0008*n*log(n)], curmol, 0, 1, None)<br />
# cmd.zoom(curmol)<br />
cmd.clip('far', -0.5*n*log(n))<br />
cmd.clip('near', -0.05*n*log(n))<br />
## Uncomment one line to render frames ##<br />
# cmd.ray(1680, 1050) # 16:10 1764000 <br />
# cmd.ray(1024, 576) # 16:9 589824<br />
# cmd.ray(800, 450) # 16:9 360000<br />
# cmd.ray(640, 360) # 16:9 230400<br />
# cmd.ray(480, 270) # 16:9 129600<br />
# cmd.ray(240, 180) # 16:9 43200 <br />
# cmd.ray(1024, 768) # 4:3 786432<br />
cmd.ray(800, 600) # 4:3 4800000<br />
# cmd.ray(640, 480) # 4:3 307200<br />
# cmd.ray(480, 360) # 4:3 172800<br />
# cmd.ray(240, 180) # 4:3 43200<br />
## Uncomment loop to repeat frames ##<br />
for i in range(0,repeat):<br />
cmd.png("imgs/"+str((n-1) * repeat + i).zfill(5)+".png")<br />
cmd.refresh()<br />
oldmol = curmol<br />
<br />
</source></div>Orpheushttps://pymolwiki.org/index.php?title=Main_Page&diff=249Main Page2005-02-19T21:45:41Z<p>Orpheus: </p>
<hr />
<div>== PyMol Wiki Home ==<br />
You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS. <br />
<br />
== Helping ==<br />
* A wiki edit/user policy is needed.<br />
* Graphic design and CSS layout: We need logos, BG images and CSS layout<br />
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki<br />
* If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].<br />
<br />
We need your help. So join today & happy editing!<br />
<br />
== Go! ==<br />
You may now add content to the wiki. This is a semi-structured wiki in that the categories are pseudo-hierarchically linked. <br />
<br />
== New ==<br />
=== Categories/Content ===<br />
If you feel we're missing a category, please find where it would most logically fit, add it to the main page via the [[Top Level Schema Policy]].<br />
<br />
== Section Layout ==<br />
Please see [[:Category:Discussion|Discussion]] for more thoughts on the site organizaiton.<br />
<br />
=== Layout Schema ===<br />
# [[:Category:News|News]]<br />
## [[:Category:News Discussion|Discussion]]<br />
## [[:Category:News PyMol Beta|PyMol Beta]]<br />
# [[:Category:Technical Issues|Technical Issues]]<br />
## [[:Category:Technical Issues Installation|Installation]]<br />
### [[:Category:Technical Issues Installation OS Dependent|OS Dependent]]<br />
#### [[:Category:Technical Issues Installation OS Dependent Linux|Linux]]<br />
#### [[:Category:Technical Issues Installation OS Dependent MAC|MAC]]<br />
#### [[:Category:Technical Issues Installation OS Dependent Windows|Windows]]<br />
# [[:Category:Launching PyMOL|Launching PyMOL]]<br />
## [[:Category:Launching PyMOL Command Line Options| Command Line Options]]<br />
## [[:Category:Launching PyMOL Launching From a Script|Launching From a Script]]<br />
# [[:Category:Using Pymol|Using PyMol]]<br />
## [[:Category:Using Pymol Mouse Controls|Mouse Controls]]<br />
## [[:Category:Using Pymol Objects and Selections|Objects and Selections]]<br />
### [[:Category:Using Pymol Objects and Selections Working with Objects|Working with Objects]]<br />
### [[:Category:Using Pymol Objects and Selections Working with Selections|Working with Selections]]<br />
### [[:Category:Using Pymol Objects and Selections Selector Quick Reference|Selector Quick Reference]]<br />
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Single-word Selectors|Single-word Selectors]]<br />
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Property Selectors|Property Selectors]]<br />
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Selection Algebra|Selection Algebra]]<br />
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Selection Macros|Selection Macros]]<br />
### [[:Category:Using Pymol Objects and Selections Representations|Representations]]<br />
#### [[:Category:Using Pymol Objects and Selections Representations Lines|Lines]]<br />
#### [[:Category:Using Pymol Objects and Selections Representations Sticks|Sticks]]<br />
#### [[:Category:Using Pymol Objects and Selections Representations Cartoon|Cartoon]]<br />
#### [[:Category:Using Pymol Objects and Selections Representations Surface|Surface]]<br />
#### [[:Category:Using Pymol Objects and Selections Representations Mesh|Mesh]]<br />
#### [[:Category:Using Pymol Objects and Selections Representations Spheres|Spheres]]<br />
#### [[:Category:Using Pymol Objects and Selections Representations Dots|Dots]]<br />
### [[:Category:Using Pymol Objects and Selections Color|Color]]<br />
### [[:Category:Using Pymol Objects and Selections Displaying Biochemical Properties|Displaying biochemical properties]]<br />
## [[:Category:Using Pymol Display Settings|Display Settings]]<br />
## [[:Category:Using Pymol Stereo 3D Display|Stereo 3D Display]] -- wrong place<br />
### [[:Category:Using Pymol Hardware Options|Hardware Options]] -- wrong place?<br />
### [[Linux XFree86 Configuration]] -- wrong place<br />
## [[:Category:Using Pymol Scenes|Scenes]]<br />
## [[:Category:Using Pymol Mouse Settings|Mouse Settings]]<br />
## [[:Category:Using Pymol Wizards|Wizards]]<br />
## [[:Category:Using Pymol Plugins |Plugins]] -- wrong place?<br />
## [[:Category:Using Pymol Ray-tracing|Ray-tracing]]<br />
## [[:Category:Using Pymol Settings Reference|Settings Reference]]<br />
## [[:Category:Using Pymol Movies and Animations|Movies and Animations]]<br />
## [[:Category:Using Pymol Structure Alignment|Structure Alignment]]<br />
## [[:Category:Using Pymol Structure Alignment Editor|Structure Alignment Editor]]<br />
# [[:Category:Commands|Command Language]]<br />
## [[:Category:Commands PyMOL Command Script|PyMOL Command Script]]<br />
## [[:Category:Commands PyMOL Python API|PyMOL Python API]]<br />
# [[:Category:Advanced Issues|Advanced Issues]]<br />
## [[:Category:Advanced Issues Modeling and Editing Structures|Modeling and editing structures]]<br />
### [[:Category:Advanced Issues Modeling and Editing Structures Editing atoms|Editing Atoms]]<br />
### [[:Category:Advanced Issues Modeling and Editing Structures Molecular Sculpting|Molecular sculpting]]<br />
### [[:Category:Advanced Issues Modeling and Editing Structures Homology Modeling|Homology modeling]]<br />
## [[:Category:Advanced Issues Image Manipulation|Image Manipulation]]<br />
### [[:Category:Advanced Issues Image Manipulation labels|labels]]<br />
### [[:Category:Advanced Issues Image Manipulation Photoshop and GIMP|Photoshop/GIMP]]<br />
### [[:Category:Advanced Issues Image Manipulation Stereo Figures|Stereo Figures]]<br />
### [[:Category:Advanced Issues Image Manipulation Publication Quatlity Images|Publication-quality images]]<br />
# [[:Category:Scripting|Scripting]]<br />
## [[:Category:Scripting Example Scripts|Example Scripts]]<br />
## [[:Category:Scripting Script Library|Script Library]]<br />
# [[:Category:Plugins|Plugins]]<br />
## [[:Category:Plugins Electrostatics and Energy Minimization| How to do electrostatics and energy minimization.]]<br />
### [[:Category:Plugins Electrostatics and Energy Minimization APBS| APBS Plugin]]<br />
## [[:Category:Plugins rtools | rtools]]<br />
## [[:Category:Plugins Tutorial|Tutorial on writing plugins]]<br />
## [[:Category:Plugins Others| Others]]<br />
# [[:Category:High-Level Applications|High-Level Applications]]<br />
## [[:Category:High-Level Applications Crystallography Applications|Crystallography Applications]]<br />
### [[:Category:High-Level Applications Symmetry|Symmetry]]<br />
### [[:Category:High-Level Applications Electron Density|Electron Density]]<br />
## [[:Category:High-Level Applications NMR Applications|NMR Applications]]<br />
### [[:Category:High-Level Applications NMR Applications Working with a Family of Structures|Working with Structure Families]]<br />
### [[:Category:High-Level Applications NMR Applications Superimposition and RMSD|Superimposition and RMSD]]<br />
### [[:Category:High-Level Applications NMR Applications NMR Restraints Analysis|NMR Restraints and Analysis]]<br />
# [[:Category:Third Party Software|Third Party Software]]<br />
## [[:Category:Third Party Software Movies|Movies]]<br />
## [[:Category:Third Party Software Codecs|Codecs]]<br />
# [[:Category:Python Integration|Python Integration]]<br />
# [[:Category:Using PyMol For Unintended Uses|Unintended Uses]] (OpenGL Object Renderer)<br />
## [[:Category:Using PyMol For Unintended Uses Arbitrary Graphics Objects| Arbitrary Graphics Objects]]<br />
# [[:Category:Uncategorized|Uncategorized]] For new pages, misplaced pages, etc.<br />
----<br />
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)<br />
----<br />
<br />
<br />
=== New! GeShi: Syntax Highlighting for Python & More ===<br />
We now have a syntax highlighter installed. It now supports something like 28 programming languages! When you paste your code simply wrap it in<br />
&lt;language_name&gt; ... code here ... &lt;/language_name&gt;. <br />
<br />
Here's an example:<br />
<pre><br />
&lt;python&gt;<br />
# axes.py<br />
from pymol.cgo import *<br />
from pymol import cmd<br />
from pymol.vfont import plain<br />
<br />
# create the axes object, draw axes with cylinders coloured red, green,<br />
#blue for X, Y and Z<br />
<br />
obj = [<br />
CYLINDER, 0., 0., 0., 50., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,<br />
CYLINDER, 0., 0., 0., 0., 50., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.,<br />
CYLINDER, 0., 0., 0., 0., 0., 50., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0,<br />
]<br />
<br />
# add labels to axes object (requires pymol version 0.8 or greater, I<br />
# believe<br />
<br />
cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])<br />
cyl_text(obj,plain,[50.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])<br />
cyl_text(obj,plain,[0.,50.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])<br />
cyl_text(obj,plain,[0.,0.,50.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])<br />
<br />
# then we load it into PyMOL<br />
cmd.load_cgo(obj,'axes')<br />
<br />
&lt;python&gt;<br />
</pre><br />
<br />
gives us the code<br />
<source lang="python"><br />
# axes.py<br />
from pymol.cgo import *<br />
from pymol import cmd<br />
from pymol.vfont import plain<br />
<br />
# create the axes object, draw axes with cylinders coloured red, green,<br />
#blue for X, Y and Z<br />
<br />
obj = [<br />
CYLINDER, 0., 0., 0., 50., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,<br />
CYLINDER, 0., 0., 0., 0., 50., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.,<br />
CYLINDER, 0., 0., 0., 0., 0., 50., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0,<br />
]<br />
<br />
# add labels to axes object (requires pymol version 0.8 or greater, I<br />
# believe<br />
<br />
cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])<br />
cyl_text(obj,plain,[50.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])<br />
cyl_text(obj,plain,[0.,50.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])<br />
cyl_text(obj,plain,[0.,0.,50.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])<br />
<br />
# then we load it into PyMOL<br />
cmd.load_cgo(obj,'axes')<br />
</source><br />
<br />
See [http://qbnz.com/highlighter/index.php The Geshi Home Page]<br />
<br />
[[User:Tree|Tree]]</div>Orpheushttps://pymolwiki.org/index.php?title=User:Orpheus&diff=235User:Orpheus2005-02-19T21:11:41Z<p>Orpheus: /* Graphics */</p>
<hr />
<div>== Tzintzuni Garcia ==<br />
University of Texas Medical Branch<br />
Department of Human Biological Chemistry and Genetics<br />
Graduate Student<br />
<br />
== Graphics ==<br />
I'll be posting some ideas for logos and graphics for this page in the next week or so.<br />
<br />
[[Image:Pymolwiki.png|PyMOL Wiki title image 1]]</div>Orpheushttps://pymolwiki.org/index.php?title=File:Pymolwiki.png&diff=2825File:Pymolwiki.png2005-02-19T21:10:46Z<p>Orpheus: pymolwiki title image 1</p>
<hr />
<div>pymolwiki title image 1</div>Orpheushttps://pymolwiki.org/index.php?title=User:Orpheus&diff=226User:Orpheus2005-02-18T00:13:06Z<p>Orpheus: /* Graphics */</p>
<hr />
<div>== Tzintzuni Garcia ==<br />
University of Texas Medical Branch<br />
Department of Human Biological Chemistry and Genetics<br />
Graduate Student<br />
<br />
== Graphics ==<br />
I'll be posting some ideas for logos and graphics for this page in the next week or so.</div>Orpheushttps://pymolwiki.org/index.php?title=User:Orpheus&diff=127User:Orpheus2005-02-18T00:12:34Z<p>Orpheus: </p>
<hr />
<div>== Tzintzuni Garcia ==<br />
University of Texas Medical Branch<br />
Department of Human Biological Chemistry and Genetics<br />
Graduate Student<br />
<br />
== Graphics ==<br />
I'll be posting some ideas for logos and graphics for this page in the next week or so.<br />
<br />
<code><br />
from math import log<br />
base = 'expt100000.1HJM_int'<br />
cmd.set('auto_zoom', 'off')<br />
cmd.set('bg_rgb', ('0', '0', '0'))<br />
cmd.set('hash_max', 240)<br />
repeat = 8 #number of frames to repeat each structure<br />
<br />
for n in range(1,501):<br />
curmol = base[0:5]+str(n).zfill(5)+base[10:]<br />
cmd.load(curmol+'.pdb')<br />
if n > 1:<br />
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)')<br />
cmd.delete(oldmol)<br />
else:<br />
cmd.orient(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')<br />
cmd.center(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')<br />
cmd.spectrum('count', 'blue_white_red', '('+curmol+')',minimum=None, maximum=None, byres=1, quiet=1)<br />
cmd.hide("lines", curmol)<br />
# cmd.show("surface", curmol)<br />
cmd.show("cartoon", curmol)<br />
cmd.set_view('\<br />
1.000000000, 0.000000000, 0.000000000,\<br />
0.000000000, 1.000000000, 0.000000000,\<br />
0.000000000, 0.000000000, 1.000000000,\<br />
0.000000000, 0.000000000, -234.718002319,\<br />
10.384142876, 15.351722717, 11.246277809,\<br />
205.446594238, 263.989440918, 0.000000000' )<br />
cmd.translate([0,0,-0.0008*n*log(n)], curmol, 0, 1, None)<br />
cmd.clip('far', -0.5*n*log(n))<br />
cmd.clip('near', -0.05*n*log(n))<br />
## Uncomment one line to render frames ##<br />
# cmd.ray(1680, 1050) # 16:10 1764000<br />
# cmd.ray(1024, 576) # 16:9 589824<br />
# cmd.ray(800, 450) # 16:9 360000<br />
# cmd.ray(640, 360) # 16:9 230400<br />
# cmd.ray(480, 270) # 16:9 129600<br />
# cmd.ray(240, 180) # 16:9 43200<br />
# cmd.ray(1024, 768) # 4:3 786432<br />
# cmd.ray(800, 600) # 4:3 4800000<br />
# cmd.ray(640, 480) # 4:3 307200<br />
# cmd.ray(480, 360) # 4:3 172800<br />
# cmd.ray(240, 180) # 4:3 43200<br />
## Uncomment loop to repeat frames ##<br />
# for i in range(0,repeat):<br />
# cmd.png("imgs/"+str((n-1) * repeat + i).zfill(5)+".png")<br />
cmd.refresh()<br />
oldmol = curmol<br />
</code></div>Orpheushttps://pymolwiki.org/index.php?title=Category:Discussion&diff=223Category:Discussion2005-02-17T22:11:14Z<p>Orpheus: /* Code Display Conventions */</p>
<hr />
<div>== Expanded Schema ==<br />
Proposal to incorporate more than just a manual into this site:<br />
<br />
# Manual<br />
## GUI<br />
## Command Script<br />
## Python API<br />
## Settings<br />
## Miscellaneous<br />
## Command Line<br />
# Meta Manual<br />
## Selections<br />
## Colors<br />
## Palettes<br />
## Writing/Running Scripts<br />
## Customizing PyMOL<br />
# Discussions<br />
## News<br />
## Development<br />
## Questions<br />
# Special Topics<br />
## Movies and Animation<br />
## biochemical calculations<br />
## NMR<br />
## Crystallography<br />
## DNA<br />
## Stereo 3D<br />
<br />
== Code Display Conventions ==<br />
This is an experiment in displaying source code:<br />
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. <br />
<pre><br />
from math import log<br />
base = 'expt100000.1HJM_int'<br />
cmd.set('auto_zoom', 'off')<br />
cmd.set('bg_rgb', ('0', '0', '0'))<br />
cmd.set('hash_max', 240)<br />
repeat = 8 #number of frames to repeat each structure<br />
<br />
for n in range(1,501):<br />
curmol = base[0:5]+str(n).zfill(5)+base[10:]<br />
cmd.load(curmol+'.pdb')<br />
if n > 1:<br />
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)')<br />
cmd.delete(oldmol)<br />
else:<br />
cmd.orient(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')<br />
cmd.center(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')<br />
cmd.spectrum('count', 'blue_white_red', '('+curmol+')',minimum=None, maximum=None, byres=1, quiet=1)<br />
cmd.hide("lines", curmol)<br />
# cmd.show("surface", curmol)<br />
cmd.show("cartoon", curmol)<br />
cmd.set_view('\<br />
1.000000000, 0.000000000, 0.000000000,\<br />
0.000000000, 1.000000000, 0.000000000,\<br />
0.000000000, 0.000000000, 1.000000000,\<br />
0.000000000, 0.000000000, -234.718002319,\<br />
10.384142876, 15.351722717, 11.246277809,\<br />
205.446594238, 263.989440918, 0.000000000' )<br />
cmd.translate([0,0,-0.0008*n*log(n)], curmol, 0, 1, None)<br />
cmd.clip('far', -0.5*n*log(n))<br />
cmd.clip('near', -0.05*n*log(n))<br />
## Uncomment one line to render frames ##<br />
# cmd.ray(1680, 1050) # 16:10 1764000<br />
# cmd.ray(1024, 576) # 16:9 589824<br />
# cmd.ray(800, 450) # 16:9 360000<br />
# cmd.ray(640, 360) # 16:9 230400<br />
# cmd.ray(480, 270) # 16:9 129600<br />
# cmd.ray(240, 180) # 16:9 43200<br />
# cmd.ray(1024, 768) # 4:3 786432<br />
# cmd.ray(800, 600) # 4:3 4800000<br />
# cmd.ray(640, 480) # 4:3 307200<br />
# cmd.ray(480, 360) # 4:3 172800<br />
# cmd.ray(240, 180) # 4:3 43200<br />
## Uncomment loop to repeat frames ##<br />
# for i in range(0,repeat):<br />
# cmd.png("imgs/"+str((n-1) * repeat + i).zfill(5)+".png")<br />
cmd.refresh()<br />
oldmol = curmol<br />
</pre></div>Orpheushttps://pymolwiki.org/index.php?title=Category_talk:Discussion&diff=2803Category talk:Discussion2005-02-17T22:05:50Z<p>Orpheus: /* FAQ and News */</p>
<hr />
<div>This layout seems better to me. Although I am not sure the News and Questions in the Discussion category are necessary, as we have the newsgroup. I would rely more on the newsgroup for news and questions.<br />
--[[User:Smg3d|Smg3d]] 14:53, 17 Feb 2005 (CST)<br />
<br />
== News & Questions ==<br />
<br />
I thought the news section could be just a central place for general news from Warren, plugin developers, or wiki site maintainers to post things concerning everyone. And the Questions area might be more of an ever growing FAQ. I think one of the things we'd like to do is add all the unique questions from the mailing list archives that are still pertinent to modern PyMOL into this wiki somewhere.<br />
<br />
--[[User:Orpheus|Orpheus]] 2004-02-17 3:14pm<br />
<br />
== FAQ and News ==<br />
<br />
I thought you meant "questions from users" in the Question category. Questions as in '''FAQ''' is definitely a '''necessity'''!<br />
<br />
For the News, it may be a good idea to have a compilation of News that are in the Newsgroup, although I guess it would mean for people to put their News to both places. Or would there be an automatic way to have News to be automatically put at both places (wiki and newsgroup)? Personnaly I would rely on the newsgroup for news, but I guess not all PyMOL users are members of the newsgroup... I am assuming that people who are newsgroup members would only come to the wiki when they want want to fix a problem, or to learn PyMOL tricks. In any case, it does not hurt, as long as information does not stop to flow in the newsgroup.<br />
--[[User:Smg3d|Smg3d]] 15:35, 17 Feb 2005 (CST)<br />
<br />
== FAQ and syntax highlighting ==<br />
<br />
I completely agree, I don't want to supplant the newsgroup, its been a great source for worldwide interactions. If we can figure it out, I think it would be nice to have say the 50 latest messages mirrored here somewhere and any good questions added to our FAQ. <br />
<br />
I think I've found a solution to add syntax highlighting to display code. I've looked into adding extensions for new tags and it seems that we could add something like a <source lang="python"></source> tag easily enough. I even found an open source project implemented in PHP no less to do syntax highlighting for us.</div>Orpheushttps://pymolwiki.org/index.php?title=Category_talk:Discussion&diff=123Category talk:Discussion2005-02-17T22:05:41Z<p>Orpheus: FAQ and syntax highlighting</p>
<hr />
<div>This layout seems better to me. Although I am not sure the News and Questions in the Discussion category are necessary, as we have the newsgroup. I would rely more on the newsgroup for news and questions.<br />
--[[User:Smg3d|Smg3d]] 14:53, 17 Feb 2005 (CST)<br />
<br />
== News & Questions ==<br />
<br />
I thought the news section could be just a central place for general news from Warren, plugin developers, or wiki site maintainers to post things concerning everyone. And the Questions area might be more of an ever growing FAQ. I think one of the things we'd like to do is add all the unique questions from the mailing list archives that are still pertinent to modern PyMOL into this wiki somewhere.<br />
<br />
--[[User:Orpheus|Orpheus]] 2004-02-17 3:14pm<br />
<br />
== FAQ and News ==<br />
<br />
I thought you meant "questions from users" in the Question category. Questions as in '''FAQ''' is definitely a '''necessity'''!<br />
<br />
For the News, it may be a good idea to have a compilation of News that are in the Newsgroup, although I guess it would mean for people to put their News to both places. Or would there be an automatic way to have News to be automatically put at both places (wiki and newsgroup)? Personnaly I would rely on the newsgroup for news, but I guess not all PyMOL users are members of the newsgroup... I am assuming that people who are newsgroup members would only come to the wiki when they want want to fix a problem, or to learn PyMOL tricks. In any case, it does not hurt, as long as information does not stop to flow in the newsgroup.<br />
--[[User:Smg3d|Smg3d]] 15:35, 17 Feb 2005 (CST)<br />
<br />
I completely agree, I don't want to supplant the newsgroup, its been a great source for worldwide interactions. If we can figure it out, I think it would be nice to have say the 50 latest messages mirrored here somewhere and any good questions added to our FAQ. <br />
<br />
I think I've found a solution to add syntax highlighting to display code. I've looked into adding extensions for new tags and it seems that we could add something like a <source lang="python"></source> tag easily enough. I even found an open source project implemented in PHP no less to do syntax highlighting for us.<br />
<br />
== FAQ and syntax highlighting ==<br />
<br />
I completely agree, I don't want to supplant the newsgroup, its been a great source for worldwide interactions. If we can figure it out, I think it would be nice to have say the 50 latest messages mirrored here somewhere and any good questions added to our FAQ. <br />
<br />
I think I've found a solution to add syntax highlighting to display code. I've looked into adding extensions for new tags and it seems that we could add something like a <source lang="python"></source> tag easily enough. I even found an open source project implemented in PHP no less to do syntax highlighting for us.</div>Orpheushttps://pymolwiki.org/index.php?title=Category_talk:Discussion&diff=122Category talk:Discussion2005-02-17T22:04:54Z<p>Orpheus: </p>
<hr />
<div>This layout seems better to me. Although I am not sure the News and Questions in the Discussion category are necessary, as we have the newsgroup. I would rely more on the newsgroup for news and questions.<br />
--[[User:Smg3d|Smg3d]] 14:53, 17 Feb 2005 (CST)<br />
<br />
== News & Questions ==<br />
<br />
I thought the news section could be just a central place for general news from Warren, plugin developers, or wiki site maintainers to post things concerning everyone. And the Questions area might be more of an ever growing FAQ. I think one of the things we'd like to do is add all the unique questions from the mailing list archives that are still pertinent to modern PyMOL into this wiki somewhere.<br />
<br />
--[[User:Orpheus|Orpheus]] 2004-02-17 3:14pm<br />
<br />
== FAQ and News ==<br />
<br />
I thought you meant "questions from users" in the Question category. Questions as in '''FAQ''' is definitely a '''necessity'''!<br />
<br />
For the News, it may be a good idea to have a compilation of News that are in the Newsgroup, although I guess it would mean for people to put their News to both places. Or would there be an automatic way to have News to be automatically put at both places (wiki and newsgroup)? Personnaly I would rely on the newsgroup for news, but I guess not all PyMOL users are members of the newsgroup... I am assuming that people who are newsgroup members would only come to the wiki when they want want to fix a problem, or to learn PyMOL tricks. In any case, it does not hurt, as long as information does not stop to flow in the newsgroup.<br />
--[[User:Smg3d|Smg3d]] 15:35, 17 Feb 2005 (CST)<br />
<br />
I completely agree, I don't want to supplant the newsgroup, its been a great source for worldwide interactions. If we can figure it out, I think it would be nice to have say the 50 latest messages mirrored here somewhere and any good questions added to our FAQ. <br />
<br />
I think I've found a solution to add syntax highlighting to display code. I've looked into adding extensions for new tags and it seems that we could add something like a <source lang="python"></source> tag easily enough. I even found an open source project implemented in PHP no less to do syntax highlighting for us.</div>Orpheushttps://pymolwiki.org/index.php?title=Category:Discussion&diff=124Category:Discussion2005-02-17T21:32:55Z<p>Orpheus: </p>
<hr />
<div>== Expanded Schema ==<br />
Proposal to incorporate more than just a manual into this site:<br />
<br />
# Manual<br />
## GUI<br />
## Command Script<br />
## Python API<br />
## Settings<br />
## Miscellaneous<br />
## Command Line<br />
# Meta Manual<br />
## Selections<br />
## Colors<br />
## Palettes<br />
## Writing/Running Scripts<br />
## Customizing PyMOL<br />
# Discussions<br />
## News<br />
## Development<br />
## Questions<br />
# Special Topics<br />
## Movies and Animation<br />
## biochemical calculations<br />
## NMR<br />
## Crystallography<br />
## DNA<br />
## Stereo 3D<br />
<br />
== Code Display Conventions ==<br />
This is an experiment in displaying source code:<br />
<pre><br />
from math import log<br />
base = 'expt100000.1HJM_int'<br />
cmd.set('auto_zoom', 'off')<br />
cmd.set('bg_rgb', ('0', '0', '0'))<br />
cmd.set('hash_max', 240)<br />
repeat = 8 #number of frames to repeat each structure<br />
<br />
for n in range(1,501):<br />
curmol = base[0:5]+str(n).zfill(5)+base[10:]<br />
cmd.load(curmol+'.pdb')<br />
if n > 1:<br />
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)')<br />
cmd.delete(oldmol)<br />
else:<br />
cmd.orient(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')<br />
cmd.center(curmol+' and name ca and (resi 56 or resi 57 or resi 58)')<br />
cmd.spectrum('count', 'blue_white_red', '('+curmol+')',minimum=None, maximum=None, byres=1, quiet=1)<br />
cmd.hide("lines", curmol)<br />
# cmd.show("surface", curmol)<br />
cmd.show("cartoon", curmol)<br />
cmd.set_view('\<br />
1.000000000, 0.000000000, 0.000000000,\<br />
0.000000000, 1.000000000, 0.000000000,\<br />
0.000000000, 0.000000000, 1.000000000,\<br />
0.000000000, 0.000000000, -234.718002319,\<br />
10.384142876, 15.351722717, 11.246277809,\<br />
205.446594238, 263.989440918, 0.000000000' )<br />
cmd.translate([0,0,-0.0008*n*log(n)], curmol, 0, 1, None)<br />
cmd.clip('far', -0.5*n*log(n))<br />
cmd.clip('near', -0.05*n*log(n))<br />
## Uncomment one line to render frames ##<br />
# cmd.ray(1680, 1050) # 16:10 1764000<br />
# cmd.ray(1024, 576) # 16:9 589824<br />
# cmd.ray(800, 450) # 16:9 360000<br />
# cmd.ray(640, 360) # 16:9 230400<br />
# cmd.ray(480, 270) # 16:9 129600<br />
# cmd.ray(240, 180) # 16:9 43200<br />
# cmd.ray(1024, 768) # 4:3 786432<br />
# cmd.ray(800, 600) # 4:3 4800000<br />
# cmd.ray(640, 480) # 4:3 307200<br />
# cmd.ray(480, 360) # 4:3 172800<br />
# cmd.ray(240, 180) # 4:3 43200<br />
## Uncomment loop to repeat frames ##<br />
# for i in range(0,repeat):<br />
# cmd.png("imgs/"+str((n-1) * repeat + i).zfill(5)+".png")<br />
cmd.refresh()<br />
oldmol = curmol<br />
</pre></div>Orpheushttps://pymolwiki.org/index.php?title=User:Orpheus&diff=126User:Orpheus2005-02-17T21:23:43Z<p>Orpheus: /* Tzintzuni Garcia */</p>
<hr />
<div>== Tzintzuni Garcia ==<br />
University of Texas Medical Branch<br />
Department of Human Biological Chemistry and Genetics<br />
Graduate Student<br />
<br />
== Graphics ==<br />
I'll be posting some ideas for logos and graphics for this page in the next week or so.</div>Orpheushttps://pymolwiki.org/index.php?title=Category:Discussion&diff=116Category:Discussion2005-02-17T21:22:47Z<p>Orpheus: </p>
<hr />
<div>I made some changes earlier to the design schema and was wondering what the community thinks so far? I also got to thinking about what we want this site to be. Should it be merely a manual or should we include news and areas for discussion on different topics such as specific uses of PyMOL? If we want to expand the scope of this site beyond just a manual, we should probably move all the basic documentation parts into their own category and have separate sections for more specific topics such as movie making, NMR, crystallography, energy calculations, etc. something like:<br />
<br />
# Manual<br />
## GUI<br />
## Command Script<br />
## Python API<br />
## Settings<br />
## Miscellaneous<br />
## Command Line<br />
# Meta Manual<br />
## Selections<br />
## Colors<br />
## Palettes<br />
## Writing/Running Scripts<br />
## Customizing PyMOL<br />
# Discussions<br />
## News<br />
## Development<br />
## Questions<br />
# Special Topics<br />
## Movies and Animation<br />
## biochemical calculations<br />
## NMR<br />
## Crystallography<br />
## DNA<br />
## Stereo 3D</div>Orpheushttps://pymolwiki.org/index.php?title=Category_talk:Discussion&diff=117Category talk:Discussion2005-02-17T21:16:04Z<p>Orpheus: /* News & Questions */</p>
<hr />
<div>This layout seems better to me. Although I am not sure the News and Questions in the Discussion category are necessary, as we have the newsgroup. I would rely more on the newsgroup for news and questions.<br />
--[[User:Smg3d|Smg3d]] 14:53, 17 Feb 2005 (CST)<br />
<br />
== News & Questions ==<br />
<br />
I thought the news section could be just a central place for general news from Warren, plugin developers, or wiki site maintainers to post things concerning everyone. And the Questions area might be more of an ever growing FAQ. I think one of the things we'd like to do is add all the unique questions from the mailing list archives that are still pertinent to modern PyMOL into this wiki somewhere.<br />
<br />
--[[User:Orpheus|Orpheus]] 2004-02-17 3:14pm</div>Orpheushttps://pymolwiki.org/index.php?title=Category_talk:Discussion&diff=113Category talk:Discussion2005-02-17T21:15:29Z<p>Orpheus: /* News & Questions */</p>
<hr />
<div>This layout seems better to me. Although I am not sure the News and Questions in the Discussion category are necessary, as we have the newsgroup. I would rely more on the newsgroup for news and questions.<br />
--[[User:Smg3d|Smg3d]] 14:53, 17 Feb 2005 (CST)<br />
<br />
== News & Questions ==<br />
<br />
I thought the news section could be just a central place for general news from Warren, plugin developers, or wiki site maintainers to post things concerning everyone. And the Questions area might be more of an ever growing FAQ. I think one of the things we'd like to do is add all the unique questions from the mailing list archives that are still pertinent to modern PyMOL into this wiki somewhere.<br />
<br />
--[[User:Orpheus]] 2004-02-17 3:14pm</div>Orpheushttps://pymolwiki.org/index.php?title=Category_talk:Discussion&diff=112Category talk:Discussion2005-02-17T21:15:16Z<p>Orpheus: /* News & Questions */</p>
<hr />
<div>This layout seems better to me. Although I am not sure the News and Questions in the Discussion category are necessary, as we have the newsgroup. I would rely more on the newsgroup for news and questions.<br />
--[[User:Smg3d|Smg3d]] 14:53, 17 Feb 2005 (CST)<br />
<br />
== News & Questions ==<br />
<br />
I thought the news section could be just a central place for general news from Warren, plugin developers, or wiki site maintainers to post things concerning everyone. And the Questions area might be more of an ever growing FAQ. I think one of the things we'd like to do is add all the unique questions from the mailing list archives that are still pertinent to modern PyMOL into this wiki somewhere.<br />
<br />
--[User:Orpheus] 2004-02-17 3:14pm</div>Orpheushttps://pymolwiki.org/index.php?title=Category_talk:Discussion&diff=111Category talk:Discussion2005-02-17T21:14:37Z<p>Orpheus: News & Questions</p>
<hr />
<div>This layout seems better to me. Although I am not sure the News and Questions in the Discussion category are necessary, as we have the newsgroup. I would rely more on the newsgroup for news and questions.<br />
--[[User:Smg3d|Smg3d]] 14:53, 17 Feb 2005 (CST)<br />
<br />
== News & Questions ==<br />
<br />
I thought the news section could be just a central place for general news from Warren, plugin developers, or wiki site maintainers to post things concerning everyone. And the Questions area might be more of an ever growing FAQ. I think one of the things we'd like to do is add all the unique questions from the mailing list archives that are still pertinent to modern PyMOL into this wiki somewhere.</div>Orpheushttps://pymolwiki.org/index.php?title=Help:Contents&diff=962Help:Contents2005-02-17T21:08:31Z<p>Orpheus: </p>
<hr />
<div>[http://meta.wikimedia.org/wiki/Help:Editing Editing Help] for the metawiki engine.</div>Orpheushttps://pymolwiki.org/index.php?title=Help:Contents&diff=109Help:Contents2005-02-17T21:08:16Z<p>Orpheus: </p>
<hr />
<div>[[http://meta.wikimedia.org/wiki/Help:Editing Editing Help]] for the metawiki engine.</div>Orpheushttps://pymolwiki.org/index.php?title=User:Orpheus&diff=115User:Orpheus2005-02-17T21:07:30Z<p>Orpheus: </p>
<hr />
<div>== Tzintzuni Garcia ==<br />
University of Texas Medical Branch<br />
Department of Human Biological Chemistry and Genetics<br />
Graduate Student<br />
<br />
== Graphics ==<br />
I'll be posting some ideas for logos and graphics for this page in the next week or so.</div>Orpheushttps://pymolwiki.org/index.php?title=Main_Page&diff=118Main Page2005-02-17T20:53:49Z<p>Orpheus: /* Layout Schema */</p>
<hr />
<div>== PyMol Wiki Home ==<br />
You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.<br />
<br />
=== Helping ===<br />
If you feel like helping out, please login and get to work. :-) For design/layout purposes you must be logged in to edit pages. We now need people to assist with<br />
<br />
* A wiki edit/user policy is needed.<br />
* Wiki schema/design/organization: Below you'll find the current layout design<br />
* Graphic design and CSS layout: We need logos, BG images and CSS layout<br />
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki<br />
* Etc...<br />
<br />
=== Editors Needed ===<br />
If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].<br />
<br />
We need your help. So join today & happy editing!<br />
<br />
[[User:Tree|Tree]]<br />
== Section Layout ==<br />
Please do not ADD any content to the site yet. Just Organize the following list as logically as possible. Here's my first go at it.<br />
<br />
Please see [[:Category:Discussion|Discussion]] for more thoughts on the site organizaiton.<br />
<br />
=== Layout Schema ===<br />
# [[:Category:News|News]]<br />
## [[:Category:Discussion|Discussion]]<br />
## [[:Category:PyMOL Beta|The Bleeding Edge]]<br />
# [[Technical Issues]] (installation, hardware)<br />
## [[Installation]]<br />
### [[OS Dependent]]<br />
#### [[Linux]]<br />
#### [[MAC]]<br />
#### [[Windows]]<br />
# [[Using the GUI]]<br />
## [[Launching PyMOL]]<br />
### [[Command Line Options]]<br />
### [[Launching From a Script]]<br />
## [[Mouse Controls]]<br />
## [[Objects and Selections]]<br />
### [[Working with Objects]]<br />
### [[Working with Selections]]<br />
### [[Selector Quick Reference]]<br />
#### [[Single-word Selectors]]<br />
#### [[Property Selectors]]<br />
#### [[Selection Algebra]]<br />
#### [[Selection Macros]]<br />
### [[Representations]]<br />
#### [[Lines]]<br />
#### [[Sticks]]<br />
#### [[Cartoon]]<br />
#### [[Surface]]<br />
#### [[Mesh]]<br />
#### [[Spheres]]<br />
#### [[Dots]]<br />
### [[Color]]<br />
### [[Displaying biochemical properties]]<br />
## [[Display Settings]]<br />
## [[Stereo 3D Display]]<br />
### [[Hardware Options]]<br />
### [[Linux XFree86 Configuration]]<br />
## [[Scenes]]<br />
## [[Mouse Settings]]<br />
## [[Wizards]]<br />
## [[Plugins]]<br />
## [[Ray-tracing]]<br />
## [[Settings Reference (all settings and what they do)]]<br />
## [[Movies and Animations]]<br />
## [[Structure Alignment]]<br />
## [[Structure Alignment Editor]]<br />
# [[:Category:Commands|Command Language]] (I added a sample category. Should we continue with something like this?) [[User:Cmoad|Charlie]]<br />
## [[PyMOL Command Script]]<br />
## [[PyMOL Python API]]<br />
# [[Advanced Issues]] (Ray tracing, settings)<br />
## [[Launching PyMOL (has been asked often)]]<br />
## [[Advanced Atom Selections]]<br />
## [[Modeling and editing structures.]]<br />
### [[Editing atoms]]<br />
### [[Molecular sculpting]]<br />
### [[Homology modeling]]<br />
## [[Image Manipulation]]<br />
### [[labels]]<br />
### [[Photoshop/GIMP]]<br />
### [[Stereo Figures]]<br />
### [[Creating publication-quality images HOWTO]]<br />
# [[Scripting]]<br />
## [[Example Scripts]]<br />
## [[Script Library]]<br />
# [[Plugins]]<br />
## [[List of Plugins]]<br />
## [[How to do electrostatics and energy minimization.]]<br />
### [[APBS Plugin]]<br />
## [[rtools Plugin]]<br />
## [[Tutorial on writing plugins]]<br />
## [[Others]]<br />
# [[High-level applications]] (Crystallography, NMR)<br />
## [[Crystallography Applications]]<br />
### [[Symmetry]]<br />
### [[Electron Density]]<br />
## [[NMR Applications]]<br />
### [[Working with a Family of Structures]]<br />
### [[Superimposition and RMSD]]<br />
### [[NMR Restraints Analysis]]<br />
# [[3rd Party Software]]<br />
## [[3rd Party Applications]]<br />
### [[Movies]]<br />
### [[Codecs]]<br />
# [[Python Integration]]<br />
# [[Using PyMol For Unintended Uses]] (OpenGL Object Renderer)<br />
## [[Arbitrary Graphics Objects]]<br />
----<br />
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)<br />
----</div>Orpheushttps://pymolwiki.org/index.php?title=Main_Page&diff=107Main Page2005-02-17T20:53:29Z<p>Orpheus: /* Layout Schema */</p>
<hr />
<div>== PyMol Wiki Home ==<br />
You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.<br />
<br />
=== Helping ===<br />
If you feel like helping out, please login and get to work. :-) For design/layout purposes you must be logged in to edit pages. We now need people to assist with<br />
<br />
* A wiki edit/user policy is needed.<br />
* Wiki schema/design/organization: Below you'll find the current layout design<br />
* Graphic design and CSS layout: We need logos, BG images and CSS layout<br />
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki<br />
* Etc...<br />
<br />
=== Editors Needed ===<br />
If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].<br />
<br />
We need your help. So join today & happy editing!<br />
<br />
[[User:Tree|Tree]]<br />
== Section Layout ==<br />
Please do not ADD any content to the site yet. Just Organize the following list as logically as possible. Here's my first go at it.<br />
<br />
Please see [[:Category:Discussion|Discussion]] for more thoughts on the site organizaiton.<br />
<br />
=== Layout Schema ===<br />
# [[Category:News|News]]<br />
## [[:Category:Discussion|Discussion]]<br />
## [[:Category:PyMOL Beta|The Bleeding Edge]]<br />
# [[Technical Issues]] (installation, hardware)<br />
## [[Installation]]<br />
### [[OS Dependent]]<br />
#### [[Linux]]<br />
#### [[MAC]]<br />
#### [[Windows]]<br />
# [[Using the GUI]]<br />
## [[Launching PyMOL]]<br />
### [[Command Line Options]]<br />
### [[Launching From a Script]]<br />
## [[Mouse Controls]]<br />
## [[Objects and Selections]]<br />
### [[Working with Objects]]<br />
### [[Working with Selections]]<br />
### [[Selector Quick Reference]]<br />
#### [[Single-word Selectors]]<br />
#### [[Property Selectors]]<br />
#### [[Selection Algebra]]<br />
#### [[Selection Macros]]<br />
### [[Representations]]<br />
#### [[Lines]]<br />
#### [[Sticks]]<br />
#### [[Cartoon]]<br />
#### [[Surface]]<br />
#### [[Mesh]]<br />
#### [[Spheres]]<br />
#### [[Dots]]<br />
### [[Color]]<br />
### [[Displaying biochemical properties]]<br />
## [[Display Settings]]<br />
## [[Stereo 3D Display]]<br />
### [[Hardware Options]]<br />
### [[Linux XFree86 Configuration]]<br />
## [[Scenes]]<br />
## [[Mouse Settings]]<br />
## [[Wizards]]<br />
## [[Plugins]]<br />
## [[Ray-tracing]]<br />
## [[Settings Reference (all settings and what they do)]]<br />
## [[Movies and Animations]]<br />
## [[Structure Alignment]]<br />
## [[Structure Alignment Editor]]<br />
# [[:Category:Commands|Command Language]] (I added a sample category. Should we continue with something like this?) [[User:Cmoad|Charlie]]<br />
## [[PyMOL Command Script]]<br />
## [[PyMOL Python API]]<br />
# [[Advanced Issues]] (Ray tracing, settings)<br />
## [[Launching PyMOL (has been asked often)]]<br />
## [[Advanced Atom Selections]]<br />
## [[Modeling and editing structures.]]<br />
### [[Editing atoms]]<br />
### [[Molecular sculpting]]<br />
### [[Homology modeling]]<br />
## [[Image Manipulation]]<br />
### [[labels]]<br />
### [[Photoshop/GIMP]]<br />
### [[Stereo Figures]]<br />
### [[Creating publication-quality images HOWTO]]<br />
# [[Scripting]]<br />
## [[Example Scripts]]<br />
## [[Script Library]]<br />
# [[Plugins]]<br />
## [[List of Plugins]]<br />
## [[How to do electrostatics and energy minimization.]]<br />
### [[APBS Plugin]]<br />
## [[rtools Plugin]]<br />
## [[Tutorial on writing plugins]]<br />
## [[Others]]<br />
# [[High-level applications]] (Crystallography, NMR)<br />
## [[Crystallography Applications]]<br />
### [[Symmetry]]<br />
### [[Electron Density]]<br />
## [[NMR Applications]]<br />
### [[Working with a Family of Structures]]<br />
### [[Superimposition and RMSD]]<br />
### [[NMR Restraints Analysis]]<br />
# [[3rd Party Software]]<br />
## [[3rd Party Applications]]<br />
### [[Movies]]<br />
### [[Codecs]]<br />
# [[Python Integration]]<br />
# [[Using PyMol For Unintended Uses]] (OpenGL Object Renderer)<br />
## [[Arbitrary Graphics Objects]]<br />
----<br />
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)<br />
----</div>Orpheushttps://pymolwiki.org/index.php?title=User:Orpheus&diff=108User:Orpheus2005-02-17T20:50:01Z<p>Orpheus: </p>
<hr />
<div> Tzintzuni Garcia<br />
University of Texas Medical Branch<br />
Department of Human Biological Chemistry and Genetics<br />
Graduate Student<br />
<br />
I'll be posting some ideas for logos and graphics for this page in the next week or so.</div>Orpheushttps://pymolwiki.org/index.php?title=User:Orpheus&diff=103User:Orpheus2005-02-17T20:49:44Z<p>Orpheus: </p>
<hr />
<div> - Tzintzuni Garcia<br />
- University of Texas Medical Branch<br />
- Department of Human Biological Chemistry and Genetics<br />
- Graduate Student<br />
<br />
I'll be posting some ideas for logos and graphics for this page in the next week or so.</div>Orpheushttps://pymolwiki.org/index.php?title=Main_Page&diff=105Main Page2005-02-17T20:28:26Z<p>Orpheus: /* Section Layout */</p>
<hr />
<div>== PyMol Wiki Home ==<br />
You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.<br />
<br />
=== Helping ===<br />
If you feel like helping out, please login and get to work. :-) For design/layout purposes you must be logged in to edit pages. We now need people to assist with<br />
<br />
* A wiki edit/user policy is needed.<br />
* Wiki schema/design/organization: Below you'll find the current layout design<br />
* Graphic design and CSS layout: We need logos, BG images and CSS layout<br />
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki<br />
* Etc...<br />
<br />
=== Editors Needed ===<br />
If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].<br />
<br />
We need your help. So join today & happy editing!<br />
<br />
[[User:Tree|Tree]]<br />
== Section Layout ==<br />
Please do not ADD any content to the site yet. Just Organize the following list as logically as possible. Here's my first go at it.<br />
<br />
Please see [[:Category:Discussion|Discussion]] for more thoughts on the site organizaiton.<br />
<br />
=== Layout Schema ===<br />
# [[:Category:News|News]]<br />
## [[:Category:Discussion|Discussion]]<br />
## [[:Category:PyMOL Beta|The Bleeding Edge]]<br />
# [[Technical Issues]] (installation, hardware)<br />
## [[Installation]]<br />
### [[OS Dependent]]<br />
#### [[Linux]]<br />
#### [[MAC]]<br />
#### [[Windows]]<br />
# [[Using the GUI]]<br />
## [[Launching PyMOL]]<br />
### [[Command Line Options]]<br />
### [[Launching From a Script]]<br />
## [[Mouse Controls]]<br />
## [[Objects and Selections]]<br />
### [[Working with Objects]]<br />
### [[Working with Selections]]<br />
### [[Selector Quick Reference]]<br />
#### [[Single-word Selectors]]<br />
#### [[Property Selectors]]<br />
#### [[Selection Algebra]]<br />
#### [[Selection Macros]]<br />
### [[Representations]]<br />
#### [[Lines]]<br />
#### [[Sticks]]<br />
#### [[Cartoon]]<br />
#### [[Surface]]<br />
#### [[Mesh]]<br />
#### [[Spheres]]<br />
#### [[Dots]]<br />
### [[Color]]<br />
### [[Displaying biochemical properties]]<br />
## [[Display Settings]]<br />
## [[Stereo 3D Display]]<br />
### [[Hardware Options]]<br />
### [[Linux XFree86 Configuration]]<br />
## [[Scenes]]<br />
## [[Mouse Settings]]<br />
## [[Wizards]]<br />
## [[Plugins]]<br />
## [[Ray-tracing]]<br />
## [[Settings Reference (all settings and what they do)]]<br />
## [[Movies and Animations]]<br />
## [[Structure Alignment]]<br />
## [[Structure Alignment Editor]]<br />
# [[:Category:Commands|Command Language]]<br />
## [[PyMOL Command Script]]<br />
## [[PyMOL Python API]]<br />
# [[Advanced Issues]] (Ray tracing, settings)<br />
## [[Launching PyMOL (has been asked often)]]<br />
## [[Advanced Atom Selections]]<br />
## [[Modeling and editing structures.]]<br />
### [[Editing atoms]]<br />
### [[Molecular sculpting]]<br />
### [[Homology modeling]]<br />
## [[Image Manipulation]]<br />
### [[labels]]<br />
### [[Photoshop/GIMP]]<br />
### [[Stereo Figures]]<br />
### [[Creating publication-quality images HOWTO]]<br />
# [[Scripting]]<br />
## [[Example Scripts]]<br />
## [[Script Library]]<br />
# [[Plugins]]<br />
## [[List of Plugins]]<br />
## [[How to do electrostatics and energy minimization.]]<br />
### [[APBS Plugin]]<br />
## [[rtools Plugin]]<br />
## [[Tutorial on writing plugins]]<br />
## [[Others]]<br />
# [[High-level applications]] (Crystallography, NMR)<br />
## [[Crystallography Applications]]<br />
### [[Symmetry]]<br />
### [[Electron Density]]<br />
## [[NMR Applications]]<br />
### [[Working with a Family of Structures]]<br />
### [[Superimposition and RMSD]]<br />
### [[NMR Restraints Analysis]]<br />
# [[3rd Party Software]]<br />
## [[3rd Party Applications]]<br />
### [[Movies]]<br />
### [[Codecs]]<br />
# [[Python Integration]]<br />
# [[Using PyMol For Unintended Uses]] (OpenGL Object Renderer)<br />
## [[Arbitrary Graphics Objects]]<br />
----<br />
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)<br />
----</div>Orpheushttps://pymolwiki.org/index.php?title=Category:Discussion&diff=114Category:Discussion2005-02-17T20:26:56Z<p>Orpheus: </p>
<hr />
<div>I made some changes earlier to the design schema and was wondering what the community thinks so far? I also got to thinking about what we want this site to be. Should it be merely a manual or should we include news and areas for discussion on different topics such as specific uses of PyMOL? If we want to expand the scope of this site beyond just a manual, we should probably move all the basic documentation parts into their own category and have separate sections for more specific topics such as movie making, NMR, crystallography, energy calculations, etc. something like:<br />
<br />
# Manual<br />
## GUI<br />
## Command Script<br />
## Python API<br />
## Settings<br />
## Miscellaneous<br />
## Command Line<br />
# Meta Manual<br />
## Selections<br />
## Colors<br />
## Palletes<br />
## Writing/Running Scripts<br />
## Customizing PyMOL<br />
# Discussions<br />
## News<br />
## Development<br />
## Questions<br />
# Special Topics<br />
## Movies and Animation<br />
## biochemical calculations<br />
## NMR<br />
## Crystallography<br />
## DNA<br />
## Stereo 3D</div>Orpheushttps://pymolwiki.org/index.php?title=Category:Discussion&diff=100Category:Discussion2005-02-17T20:25:09Z<p>Orpheus: </p>
<hr />
<div>I made some changes earlier to the design schema and was wondering what the community thinks so far? I also got to thinking about what we want this site to be. Should it be merely a manual or should we include news and areas for discussion on different topics such as specific uses of PyMOL? If we want to expand the scope of this site beyond just a manual, we should probably move all the basic documentation parts into their own category and have separate sections for more specific topics such as movie making, NMR, crystallography, energy calculations, etc. something like:<br />
<br />
Manual<br />
- GUI<br />
- Command Script<br />
- Python API<br />
- Settings<br />
- Miscellaneous<br />
- Command Line<br />
Meta Manual<br />
- Selections<br />
- Colors<br />
- Palletes<br />
- Writing/Running Scripts<br />
- Customizing PyMOL<br />
Discussions<br />
- News<br />
- Development<br />
- Questions<br />
Special Topics<br />
- Movies and Animation<br />
- biochemical calculations<br />
- NMR<br />
- Crystallography<br />
- DNA</div>Orpheushttps://pymolwiki.org/index.php?title=Main_Page&diff=95Main Page2005-02-17T18:20:59Z<p>Orpheus: /* Layout Schema */</p>
<hr />
<div>== PyMol Wiki Home ==<br />
You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.<br />
<br />
=== Helping ===<br />
If you feel like helping out, please login and get to work. :-) For design/layout purposes you must be logged in to edit pages. We now need people to assist with<br />
<br />
* A wiki edit/user policy is needed.<br />
* Wiki schema/design/organization: Below you'll find the current layout design<br />
* Graphic design and CSS layout: We need logos, BG images and CSS layout<br />
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki<br />
* Etc...<br />
<br />
=== Editors Needed ===<br />
If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].<br />
<br />
We need your help. So join today & happy editing!<br />
<br />
[[User:Tree|Tree]]<br />
== Section Layout ==<br />
Please do not ADD any content to the site yet. Just Organize the following list as logically as possible. Here's my first go at it.<br />
<br />
=== Layout Schema ===<br />
# [[:Category:News|News]]<br />
## [[:Category:Discussion|Discussion]]<br />
## [[:Category:PyMOL Beta|The Bleeding Edge]]<br />
# [[Technical Issues]] (installation, hardware)<br />
## [[Installation]]<br />
### [[OS Dependent]]<br />
#### [[Linux]]<br />
#### [[MAC]]<br />
#### [[Windows]]<br />
# [[Using the GUI]]<br />
## [[Launching PyMOL (has been asked often)]]<br />
## [[Mouse Controls]]<br />
## [[Objects and Selections]]<br />
### [[Working with Objects]]<br />
### [[Working with Selections]]<br />
### [[Representations]]<br />
#### [[Lines]]<br />
#### [[Sticks]]<br />
#### [[Cartoon]]<br />
#### [[Surface]]<br />
#### [[Mesh]]<br />
#### [[Spheres]]<br />
#### [[Dots]]<br />
### [[Color]]<br />
### [[Displaying biochemical properties]]<br />
## [[Display Settings]]<br />
## [[Stereo 3D Display]]<br />
### [[Hardware Options]]<br />
### [[Linux XFree86 Configuration]]<br />
## [[Scenes]]<br />
## [[Mouse Settings]]<br />
## [[Wizards]]<br />
## [[Plugins]]<br />
## [[Ray-tracing]]<br />
## [[Settings Reference (all settings and what they do)]]<br />
## [[Movies and Animations]]<br />
## [[Structure Alignment]]<br />
## [[Structure Alignment Editor]]<br />
# [[:Category:Commands|Command Language]]<br />
## [[PyMOL Command Script]]<br />
## [[PyMOL Python API]]<br />
# [[Advanced Issues]] (Ray tracing, settings)<br />
## [[Launching PyMOL (has been asked often)]]<br />
## [[Advanced Atom Selections]]<br />
## [[Modeling and editing structures.]]<br />
### [[Editing atoms]]<br />
### [[Molecular sculpting]]<br />
### [[Homology modeling]]<br />
## [[Image Manipulation]]<br />
### [[labels]]<br />
### [[Photoshop/GIMP]]<br />
### [[Stereo Figures]]<br />
### [[Creating publication-quality images HOWTO]]<br />
# [[Scripting]]<br />
## [[Example Scripts]]<br />
## [[Script Library]]<br />
# [[Plugins]]<br />
## [[List of Plugins]]<br />
## [[How to do electrostatics and energy minimization.]]<br />
### [[APBS Plugin]]<br />
## [[rtools Plugin]]<br />
## [[Tutorial on writing plugins]]<br />
## [[Others]]<br />
# [[High-level applications]] (Crystallography, NMR)<br />
## [[Crystallography Applications]]<br />
### [[Symmetry]]<br />
### [[Electron Density]]<br />
## [[NMR Applications]]<br />
### [[Working with a Family of Structures]]<br />
### [[Superimposition and RMSD]]<br />
### [[NMR Restraints Analysis]]<br />
# [[3rd Party Software]]<br />
## [[3rd Party Applications]]<br />
### [[Movies]]<br />
### [[Codecs]]<br />
# [[Python Integration]]<br />
# [[Using PyMol For Unintended Uses]] (OpenGL Object Renderer)<br />
## [[Arbitrary Graphics Objects]]<br />
----<br />
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)<br />
----</div>Orpheushttps://pymolwiki.org/index.php?title=Main_Page&diff=89Main Page2005-02-17T18:07:58Z<p>Orpheus: /* Layout Schema */</p>
<hr />
<div>== PyMol Wiki Home ==<br />
You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.<br />
<br />
=== Helping ===<br />
If you feel like helping out, please login and get to work. :-) For design/layout purposes you must be logged in to edit pages. We now need people to assist with<br />
<br />
* A wiki edit/user policy is needed.<br />
* Wiki schema/design/organization: Below you'll find the current layout design<br />
* Graphic design and CSS layout: We need logos, BG images and CSS layout<br />
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki<br />
* Etc...<br />
<br />
=== Editors Needed ===<br />
If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].<br />
<br />
We need your help. So join today & happy editing!<br />
<br />
[[User:Tree|Tree]]<br />
== Section Layout ==<br />
Please do not ADD any content to the site yet. Just Organize the following list as logically as possible. Here's my first go at it.<br />
<br />
=== Layout Schema ===<br />
# [[Technical Issues]] (installation, hardware)<br />
## [[Installation]]<br />
### [[OS Dependent]]<br />
#### [[Linux]]<br />
#### [[MAC]]<br />
#### [[Windows]]<br />
# [[Using the GUI]]<br />
## [[Launching PyMOL (has been asked often)]]<br />
## [[Mouse Controls]]<br />
## [[Objects and Selections]]<br />
### [[Working with Objects]]<br />
### [[Working with Selections]]<br />
### [[Representations]]<br />
#### [[Lines]]<br />
#### [[Sticks]]<br />
#### [[Cartoon]]<br />
#### [[Surface]]<br />
#### [[Mesh]]<br />
#### [[Spheres]]<br />
#### [[Dots]]<br />
### [[Color]]<br />
### [[Displaying biochemical properties]]<br />
## [[Display Settings]]<br />
## [[Stereo 3D Display]]<br />
### [[Hardware Options]]<br />
### [[Linux XFree86 Configuration]]<br />
## [[Scenes]]<br />
## [[Mouse Settings]]<br />
## [[Wizards]]<br />
## [[Plugins]]<br />
## [[Ray-tracing]]<br />
## [[Settings Reference (all settings and what they do)]]<br />
## [[Movies and Animations]]<br />
## [[Structure Alignment]]<br />
## [[Structure Alignment Editor]]<br />
# [[:Category:Commands|Command Language]]<br />
## [[PyMOL Command Script]]<br />
## [[PyMOL Python API]]<br />
# [[Advanced Issues]] (Ray tracing, settings)<br />
## [[Launching PyMOL (has been asked often)]]<br />
## [[Advanced Atom Selections]]<br />
## [[Modeling and editing structures.]]<br />
### [[Editing atoms]]<br />
### [[Molecular sculpting]]<br />
### [[Homology modeling]]<br />
## [[Image Manipulation]]<br />
### [[labels]]<br />
### [[Photoshop/GIMP]]<br />
### [[Stereo Figures]]<br />
### [[Creating publication-quality images HOWTO]]<br />
# [[Scripting]]<br />
## [[Script Library]]<br />
# [[Plugins]]<br />
## [[List of Plugins]]<br />
## [[How to do electrostatics and energy minimization.]]<br />
### [[APBS Plugin]]<br />
## [[rtools Plugin]]<br />
## [[Tutorial on writing plugins]]<br />
## [[Others]]<br />
# [[High-level applications]] (Crystallography, NMR)<br />
## [[Crystallography Applications]]<br />
### [[Symmetry]]<br />
### [[Electron Density]]<br />
## [[NMR Applications]]<br />
### [[Working with a Family of Structures]]<br />
### [[Superimposition and RMSD]]<br />
### [[NMR Restraints Analysis]]<br />
# [[3rd Party Software]]<br />
## [[3rd Party Applications]]<br />
### [[Movies]]<br />
### [[Codecs]]<br />
# [[Python Integration]]<br />
# [[Using PyMol For Unintended Uses]] (OpenGL Object Renderer)<br />
## [[Arbitrary Graphics Objects]]<br />
----<br />
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)<br />
----</div>Orpheushttps://pymolwiki.org/index.php?title=User:Orpheus&diff=102User:Orpheus2005-02-17T00:04:47Z<p>Orpheus: </p>
<hr />
<div>PyMol Rocks!<br />
<br />
<br />
I'll be posting some ideas for logos and graphics for this page in the next week or so.<br />
<br />
Is there any way to pop up a window before your login session times out?</div>Orpheus