From: Ashar Malik (
Date: Tue Aug 16 2022 - 12:53:49 CDT


So there are various keywords that you can group together.

For instance you can say something like:

name OG and within 5 of resid 5 and name OG

Here residue 5’s atom OG is your reference

The selection will select all OG within 5A of OG in residue 5. It will
include the reference as well. To exclude reference - using ‘exwithin’
instead of within.

Hope this helps.


On Wed, Aug 17, 2022 at 1:21 AM Huang, Caleb <> wrote:

> Hello,
> I'd like to select all atoms that are within 3A of another atom with the
> same identifier. More specifically, I want to select all serine oxygen
> "OG" that are within 3A of a different "OG". The following commands command
> doesn't work, as it selects all OGs, not just OG's that are within 3A of
> other OGs: name OG and within 3 of (name OG). I'm thinking that this what
> the command should look like: name OG and within 3 of (DIFFERENT name OG)
> -- except I'm not sure how to specify "different" OG with the same
> identifier.
> Any help would be appreciated!
> -Caleb