[Chimera-users] defining a putative binding site

Elaine Meng meng at cgl.ucsf.edu
Wed Feb 18 09:00:22 PST 2009

Hi Francesco,
Your approach sounds OK to me.  Then if you want a list of the  
selected residues, choose "Actions... Write List" and in that dialog,  
change the little menus at the bottom to Write "selected"  
"residues" (I assume you didn't want each atom to be listed).  You  
can either click Log to send the list to the Reply Log or save the  
list to a file.
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 18, 2009, at 12:41 AM, Francesco Pietra wrote:

> Hi:
> I need to define a putative binding site for a smaller protein upon a
> larger one. The task is creating a table of likely interactions
> between residues of the larger proteinseparated by less than 5 A from
> those of the smaller protein. Deriving from molecular dynamics, all
> residues for both proteins are in the same pdb file, alongside lipid,
> water, etc.
> I wonder whether the most appropriate way is to separate in two
> different pdb files the lines belonging to the two different proteins.
> Then:
> sel #0:20,30-40,55 & #1:1701-1793 z<5
> where "0" is the larger and "1" is the smaller protein. If OK, can the
> results be obtained in a table form?
> Thanks
> francesco pietra

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