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 <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. Thanks! Mike