[Chimera-users] automated selection of most N-terminal residue in model

Elaine Meng meng at cgl.ucsf.edu
Fri Jan 6 14:00:09 PST 2012

Hi Michel,
I can't think of any way to do it with Chimera commands.  For residue ranges the words "start" and "end" can be used, but they can't be used alone, only in ranges, for example:

sel :start-12
sel :100-end.A

Another semi-dead end is the atom attribute serialNumber.  If the first residue is an amino acid, typically the first atom is the N of that residue.  The first atom can be selected regardless of residue number with:

sel @/serialNumber=1  

However, that would only get the start of the first chain in the file; you wouldn't know the serial numbers to use for the other chains.

There is probably some ingenious way of doing it in Python, but that is beyond my skill set -- sorry,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 6, 2012, at 11:13 AM, michel dedeo wrote:

> Hi,
> I'm trying to measure the distance between the N-termini (or the first known residue) of a batch of dimeric proteins. The two proteins are different chains. I know how to do this by hand, but am exploring different ways to script it. It may be best to avoid using chimera entirely, but I thought I'd check to see if anyone knows a clever way to select the residue closest to the N-terminus when it's not residue #1.
> Thanks for your help.
> Michel 

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