[chimerax-users] measure neighboring distance of histidine side chain

[Elaine Meng]

Hello Hong, 
you can limit the contacts calculation to only include histidine residues, or specific atoms in histidine residues (e.g. if you only cared about the sidechain nitrogens, or only the alpha-carbons).  Example:

contacts :his at nd1,ne2 restrict :his at nd1,ne2 distanceOnly 500 log true

...(plus any other options you wanted) to list all-by-all distances <500 Angstroms between histidine sidechain nitrogens in the Log. 

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


> On Apr 5, 2022, at 9:20 AM, HONG ZHAN via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear all, 
> 
> I am interested to get a list of distances between histidine residues in my built model. Because I would like to see which crosslinker can potentially help to maintain the structure better during purification. 
> 
> I have noticed that I can measure one residue in chain A to all other atoms in chain B using contact function, however, I want to get a list of distances between any histidine imidazole (neighboring distance), is there a way to do that in ChimeraX?
> 
> Super thanks in advance. 
> 
> Best,
> Hong