[Chimera-users] Labels of Metal atoms
pett at cgl.ucsf.edu
Tue Feb 15 14:40:52 PST 2011
On Feb 11, 2011, at 4:20 PM, Tom Goddard wrote:
> Hi Mike,
> I see your test file contains Cu1 and Chimera shows that in a
> label as CU1 with all upper case. That surprises me. Our expert on
> that Eric Pettersen can explain it next week. You may be right that
> Chimera knows the atomic elements and could selectively capitalize
> labels according to your preferences when the atom name matches the
> element symbol. Again it is something Eric can advise on.
The upper-casing has been there since "time immemorial" (i.e. Greg
doesn't remember why he wrote the code that way ;-) ). I could take
it out in the 1.6 daily build and see what happens. It would only
affect non-standard PDB files, since all RCSB PDB files use upper case
exclusively. The possible negative consequence would be that if some
program generates PDB files where the backbone atoms are "ca", "n",
"c", etc. then Chimera would no longer recognize them as backbone and
would not depict them with ribbons, would not automatically get their
atom types correct, etc.
Are there major programs out there that generate lower case atom
names? Beats me. I can't think of any off the top of my head. If
anyone can, please chime in! I guess I'll remove the upper casing (in
the 1.6 build) if no one does...
UCSF Computer Graphics Lab
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