[Chimera-users] Selecting residues with zones when reference is absent

Elaine Meng meng at cgl.ucsf.edu
Mon Sep 16 10:44:42 PDT 2019

Hello Carlos,
Try these commands:

select ligand & nucleic acid z<10
~select protein z<10

I tried it on examples of nucleic acid structures with ligand and with and without protein: 6raw and 6gld, respectively.

If you want just one line of commands, you can put them together with a semicolon between.
I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 13, 2019, at 11:52 AM, Carlos G. Oliver <cgoliver at protonmail.com> wrote:
> Hello,
> I would like to select all ligands that are within a distance of nucleic acids but above a distance from proteins.
> The selection command I have so far is:
> `select nucleic acid z<10 & protein z>10 & ligand`
> This works for PDBs that contain both nucleic acids and protein.
> However, some will only contain nucleic acids, and in this case the `protein z>10` condition will result in an empty selection even when there is a valid ligand.
> I was wondering if there was a way to check whether the model contains protein to run a different selection command for each case, or to use a different selection command which handles both cases.
> Thanks!
> Carlos G. Oliver

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