[Chimera-users] viewing the model

Elaine Meng meng at cgl.ucsf.edu
Mon Apr 27 08:01:03 PDT 2020

Hi Dmitry,
Of course you can hide any parts of the atomic structure.  You just need to know some way to specify the parts you want, e.g. maybe simply "ligand" will work, or you may have to figure out the residue names and/or atom numbers.

You can also do this with the menu, but shorter to give example commands, e.g. say your structure is #0 and "ligand" works in your case to show the parts you want:

~display #0
~ribbon #0
display #0 & ligand

If "ligand" doesn't automatically identify the part you want, you'd have to use residue name(s) or number(s), e.g.

display #0:CAR,RET
display #0:1346.A,254-288.B

.... the latter example showing residue 1346 of chain A and residues 254-288 of chain B.  All these command-line specifiers, including ligand, are explained in the "atom specification" page.

You could also take a look at "getting started" tutorials for basic manipulation/specification of atomic structures.

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

> On Apr 27, 2020, at 1:31 AM, Dmitry A. Semchonok <semchonok at gmail.com> wrote:
> Dear colleagues,
> I want to look closely into the map structure that has pigment molecules: chlorophylls, carotenoids, etc.
> Is there an option to show the chlorophylls only, the carotenoids, and hide all the other elements?
> Or I need to delete everything in the PDB except the one I am interested in? 
> Thank you
> Sincerely,
> Dmitry

More information about the Chimera-users mailing list