[chimerax-users] select atoms nearest to chain

[Pranav Shah]

Thanks Elaine! Will give these a go!
:)
Best,
Pranav
--
Pranav Shah
Postdoctoral Research Fellow.

Division of Structural Biology,
Wellcome Trust Centre for Human Genetics,
University of Oxford,
Roosevelt Drive, Oxford OX3 7BN,
UK

On Wed, May 11, 2022 at 12:52 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:
>
> 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
>