Brilliant!

Thank you Elaine.

rob

From: Elaine Meng <meng@cgl.ucsf.edu>
Date: Tuesday, August 13, 2024 at 3:39 PM
To: Kotin, Robert <Robert.Kotin@umassmed.edu>
Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu>, Robert Kotin <kotinr@mit.edu>
Subject: specifying residues in Chimera

Hi Robert,
This is explained in the "atom specification" page -- there are lots of ways to specify atoms, but one way is that  ":" means residue name or number, and if you don't specify the chain it will already include that residue number in all chains. 

Atom specification is the command-line specification of atoms, as could be used in any command that refers to atoms: color, display, repr, etc.:
<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fframeatom_spec.html&data=05%7C02%7CRobert.Kotin%40umassmed.edu%7C800b2f654ee74ae0713e08dcbbcfa374%7Cee9155fe2da34378a6c44405faf57b2e%7C0%7C0%7C638591747710018315%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=tRdMp0umLHbRkMIIli1N2PAmrsJGgvRIEFK%2BmZ9htu8%3D&reserved=0>
<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fatom_spec.html%23basic&data=05%7C02%7CRobert.Kotin%40umassmed.edu%7C800b2f654ee74ae0713e08dcbbcfa374%7Cee9155fe2da34378a6c44405faf57b2e%7C0%7C0%7C638591747710029881%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=RXHlOMihnLh4VZlDB3pkl%2B1ZdxljSiaDTDen8fhvgjQ%3D&reserved=0>

Example commands:

open biounitID:1lp3
display :314
repr sphere :314
color red,a :314

See help pages for individual commands for their usage (syntax), which will include "atomspec" as detailed in the links above.
<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fframecommand.html&data=05%7C02%7CRobert.Kotin%40umassmed.edu%7C800b2f654ee74ae0713e08dcbbcfa374%7Cee9155fe2da34378a6c44405faf57b2e%7C0%7C0%7C638591747710036497%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=bMryR%2FqlLjefUM45ws5VFe6HBsZ%2Fv6FQK0atS1wA4BQ%3D&reserved=0>

You could also select them, e.g.

select :314

...and then use the Actions menu to act upon them, if you don't want to remember the individual commands, then

~select

to deselect them.

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

> On Aug 13, 2024, at 11:50 AM, Kotin, Robert via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
>
> Good afternoon – I’d appreciate advise for virus capsid viewing. Adeno-associated viruse structures, e.g., 1lp3, consist of the asymmetric unit repeated 60x to form the icosahedral capsid (T=1). I’d like to highlight the equivalent residue in each of the 60 subunits but haven’t figured out how to do that (except by manually going through each of the 60 chains).
>  Please let me know if there are commands that can specify the residue in chains 1, 2, 3,…60.
>  Thank you
> Robert Kotin
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