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
>%f"%min_score-0.0001,representation="spheres")
cmd.spectrum("b","blue_red",selection=include,minimum=min_score,maximum=max_score)
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@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
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.
Thanks!
Mike