[Chimera-users] Transition from PyMol

R Michael Sivley mike.sivley at vanderbilt.edu
Wed May 14 10:23:40 PDT 2014

I'm attempting to transition from Chimera to PyMol and I'm struggling to 
reproduce the results of a visualization script. The script maps numeric 
values onto certain residues in a protein structure. Those residues are 
marked by spheres, and those spheres are colored by spectrum according 
to the residue value.

In PyMol I overwrite the atom bfactors, and then display the CA of 
annotated residues as a sphere, colored by spectrum. The PyMol code 
(post-bfactor overwrite):
cmd.show(selection="name CA and br. b 

In Chimera I've generated an attribute file, and used defattr to assign 
values to residues. I get the spheres by creating spheres centered on 
the CA atom of the annotated residues:
rc("open %(struct_loc)s"%params)
rc("defattr %(tempf)s"%params)
rc("ribcolor dark grey") # temporary
for resi in params['resis']:
   rc("shape sphere center %s at CA radius 1 color grey"%resi[0])
rc("rangecolor %(anno)s %(minval)s blue %(maxval)s red"%params)

At this point, I can color the residues themselves using their attribute 
values, but I can't color the spheres, because they don't contain the 
information necessary to color them. I've uploaded the PyMol and Chimera 
generated images to imgur here:
PyMol: http://imgur.com/a/GVfWi#0
Chimera: http://imgur.com/a/GVfWi#1
<http://imgur.com/a/n1PNl#1>Any help in reproducing the PyMol image in 
Chimera would be much appreciated. I haven't begun working on 
orientation (PyMol's `orient` equivalent), but any quick tips there 
would certainly be helpful as well.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20140514/60219c81/attachment.html>

More information about the Chimera-users mailing list