[Chimera-users] Help for USCF chimera

[Elaine Meng]

Hi Cindy,
It is not possible to give you an exact command without having your data to examine.  The reason is that how to specify something in the command line depends on how it is named in your input PDB file, i.e. what chain ID and/or residue numbers are in the file.  Also I don't know specifically what you want to do with the "identified" antigen residues - label them? list them?  However, I will try to give you some examples.

If you have already selected the antibody residues of interest (i.e. they are shown with green outlines), then for example if the antigen is residues 1-50 of chain B, you could label the antigen residues within 5A of the selected atoms with command:

rlabel :1-50.B & sel zr<5

...meaning residue-label residues 1-50 of chain B with any atom within 5A of the current selection

Or you could select the residues instead and write a list to a text file, for example:

select :1-50.B & sel zr<5
writesel browser

...where the second command above opens a file browser window so that you can specify interactively the text file name/location.

There are many Chimera tutorials and a complete User Guide:
<https://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html>
<https://www.rbvi.ucsf.edu/chimera/tutorials.html>
<https://www.rbvi.ucsf.edu/chimera/current/docs/UsersGuide/framecore.html>

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

> On Mar 10, 2022, at 3:59 AM, cindy g via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Good morning,
> 
> By Uscf chimera I have a complex with an antibody and an antigen.
> After determining the predicted paratopes and highlighting only their side chains, I would like to identify the side chains of the amino acids of the antigen which are in a zone <5A from the side chains of the predicted paratopes.
> 
> I don't know how to do it with command lines or anything.
> 
> Thank you in advance for your help
> 
> Cordially