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

Carlos G. Oliver cgoliver at protonmail.com
Mon Sep 16 11:29:36 PDT 2019

Hello Elaine,

That is perfect. Thank you very much!


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‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
On Monday, September 16, 2019 1:44 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
> ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> 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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