[Chimera-users] Displaying atoms within a distance

[Tom Goddard]

Hi Nikolay,

~disp solvent
disp protein z<3

The word protein can be used to designate all the amino acids.

  Tom



On Apr 21, 2012, at 9:54 AM, Elaine Meng wrote:

> 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:
> 
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
> 
> 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
> -----
> 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)
> <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/quickref.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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