[Chimera-users] Letter Reference for Amino Acid Atoms

[Elaine Meng]

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.
Best,
Elaine
-----
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
                      http://www.cgl.ucsf.edu/home/meng/index.html



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