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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. <br>
<br>
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):<br>
<tt>cmd.show(selection="name CA and br. b
>%f"%min_score-0.0001,representation="spheres")</tt><tt><br>
</tt><tt>cmd.spectrum("b","blue_red",selection=include,minimum=min_score,maximum=max_score)</tt><br>
<br>
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:<br>
<tt>rc("open %(struct_loc)s"%params)</tt><tt><br>
</tt><tt>rc("defattr %(tempf)s"%params)</tt><tt><br>
</tt><tt>rc("ribcolor dark grey") # temporary</tt><tt><br>
</tt><tt>for resi in params['resis']:</tt><tt><br>
</tt><tt> rc("shape sphere center %s@CA radius 1 color
grey"%resi[0])</tt><tt><br>
</tt><tt>rc("rangecolor %(anno)s %(minval)s blue %(maxval)s
red"%params)</tt><br>
<br>
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:<br>
PyMol: <a class="moz-txt-link-freetext" href="http://imgur.com/a/GVfWi#0">http://imgur.com/a/GVfWi#0</a><br>
Chimera: <a class="moz-txt-link-freetext" href="http://imgur.com/a/GVfWi#1">http://imgur.com/a/GVfWi#1</a><a
href="http://imgur.com/a/n1PNl#1"><br>
</a>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.<br>
<br>
Thanks!<br>
Mike<br>
<br>
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