[Chimera-users] Letter Reference for Amino Acid Atoms

Elaine Meng meng at cgl.ucsf.edu
Mon Feb 23 10:09:12 PST 2009

Hi Sarah,
The part inside the parentheses is the atom name, as read from the  
input file.  I can tell because these are the standard atom names used  
in PDB files.

However, I don't understand what where/what you are scrolling over or  
in which program (how you got those strings with parentheses in them)  
-- when I put the mouse over an atom in Chimera, I get information  
that does not contain any parentheses.
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Feb 17, 2009, at 9:01 PM, Sarah Himes wrote:

> Hi,
> My name is Sarah Himes.  I'm a graduate student at the University of  
> Maryland.  I'm researching alkaline phosphatase for an advanced  
> course.  I'm using the file 1ALK in Chimera.  I'm pretty familiar  
> with Chimera but I had a question regarding the letter notation of  
> amino acid atoms when you scroll over them.
> Here are some examples:
> His370 (NE2)
> Ser102 (CB)
> Ser102 (N)
> Asp327 (OD1)
> Asp327 (OD2)
> Glu322 (OE2)
> My question is, what do the letters in parentheses mean, what do  
> they correspond to?  When these letters show up in Chimera, there  
> are no parentheses.
> I look forward to hearing from you shortly.  Thank you for your time.
> Sincerely,
> Sarah Himes
> shimes at umd.edu
> 240-285-1251

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