[Chimera-users] Displaying atoms within a distance

Elaine Meng meng at cgl.ucsf.edu
Sat Apr 21 09:54:48 PDT 2012

Hi Nikolay,
The "atom specification" part of many commands (color, display, etc.) can include zones, for example:

display :lys z<3

... to display residues with any atom within 3 angstroms of lysine.  

Atom specification can be done in many ways ranging from simple to complex, so it is explained separately from the individual commands:


See the "zones" section of that page.  You can use za instead of z for atom-based rather than residue-based cutoff, and > instead of < for the complementary set.  You can also combine specifications, for example:

display solvent & :lys z<3

... to display residues classified as solvent (could use :hoh instead) that have any atom within 3 angstroms of lysine. 

display solvent & :23.a z<3.5

... solvent residues within 3.5 angstroms of residue 23 in chain A

It is also possible to use the menus (see Select... Zone) but it would take more steps and commands are much better for complex specifications.  I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

P.S. there are more atom-spec examples in the page linked above, as well as the Chimera Quick Reference (PDF)

On Apr 21, 2012, at 7:33 AM, Nikolay Igorovich Rodionov wrote:

> Hi everyone,
> I am trying to display waters within a set distance from a solvated protein.  Can someone please tell me how I can use the display or show commands to selectively show only the residues that are within a specific distance from a residue type? I’ve looked at the chimera manual and I am still confused on how these commands function.
> Thank you,
> Nikolay Rodionov

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