[Chimera-users] how to obtain information regarding complexes

Elaine Meng meng at cgl.ucsf.edu
Thu Jul 18 13:08:30 PDT 2019

Hello Farhan,
You can specify atoms by distance zones in the command line.

For example, to select atoms in chain B that are within 5.5 Angstroms of atoms in chain A:

select :.B & :.A za<5.5

or use “zr” instead of “za” to select the whole residues instead of only parts of residues.

Remember that solvent, ions etc. could also be in the chains. If you want to consider protein only you could just delete all the other stuff first, e.g. command

delete ~protein

Then you can write a list of the selected atoms or residues using command “writesel" or menu: Actions… Write List.

These are fairly basic things.  For your research in general, you might want to search documentation (menu: Help… Search Documentation) or take a look at some of the tutorials, like “getting started” and “structure analysis and comparison”:


I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 18, 2019, at 9:05 AM, Quadir, Farhan (MU-Student) <fqg7h at mail.missouri.edu> wrote:
> Hello,
> I am relatively new to chimera. I am stuck with a problem of how to perform the following from a pdb file which contains multiple chains:
> 	• I would like to find regions which are 5.0 Angstroms or less between selected chains.
> 	• After obtaining that I would like to get from (1) a list of the residues and their positions in the chain that are interacting with each other inter-chainwise. 
> Regards,
> Farhan Quadir

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