[Chimera-users] Labels of Metal atoms

Eric Pettersen 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...


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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