[chimerax-users] select atoms nearest to chain

[Elaine Meng]

Hi Pranav,
If you mean a command, then if residue-based (i.e. you want whole residues):

select ((/A & /B :<4) | (/B & /A :<4))

The thing in the middle is a vertical bar, not a letter or number.  See how to specify zones and combinations:

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#zones>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#combinations>

If atom-based instead of residue-based use @< instead of :<, and if you
don't want to include nonpolymer stuff like ligands or waters, that can also be arranged:

select ((/A & /B :<4) | (/B & /A :<4)) & ::polymer_type>0

See specifying attributes like polymer_type:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#attributes>

I'm told that in the very newest daily build there is also a GUI called from the menu: Select... Contacts that does something like the second command above, but I haven't had time to try it yet myself or document it.

To list the selected residues in the Log, could use command:

info residues sel

see
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html#residues> 

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

> On May 10, 2022, at 4:40 PM, Pranav Shah via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Elaine,
> How does one select atoms on one chain that are close to another chain
> based on a distance cut off?
> for eg: chain A and B form an interface. I now want to know which
> residues on chain A fall within a distance of 4Å from chain B and vice
> versa.
> Best,
> Pranav