[Chimera-users] identifying and counting selected residues

Elaine Meng meng at cgl.ucsf.edu
Wed Mar 31 08:21:58 PDT 2021

Greetings Smit,
You can just use the "select" command with these amino acid categories, for example:

select polar
select nonpolar
select hydrophobic


.... and then the Selection Inspector says how many residues are selected.  You can open this tool from the menu (Actions... Inspect) or by clicking the magnifying-glass icon near the bottom right corner of the Chimera window, 

and just keep that tool open the whole time.  Then when you use the different select commands, it will say near the top of that dialog how many residues and atoms are selected.

There are beginner tutorials for starting to use commands, for example 

...and the "working with commands" section in:

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

> On Mar 31, 2021, at 12:29 AM, Smit Patel <patelsmit11103 at gmail.com> wrote:
> Respected sir/ma’am,
> Greetings for the day!
> I’m new user of chimera tool and I don’t know many functions related to command line. So my question is how to identify and count polar, nonpolar , hydrophobic residues in a given protein using command line.
> Like in gui I performed selectàresidueàamino acid categoryàpolar or hydrophobic. So how to covert this process into the code using command line and get the count of the residues which are selected hydrophobic/polar?
> It would be very grateful if you could advise me how to code the command line. 
> Thank you,
> Regards 
> Smit  

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