[chimerax-users] mapping out water channels in chimerax

[Elaine Meng]

Hi Noor,
Maybe I'm misunderstanding the question, but why not just calculate all H-bonds among all the water molecules?   Or, maybe all the water molecules within a certain distance from the protein or any specific part of the structure.  Or, if you only want those 14 water molecules, you can just calculate all of their H-bonds if you can list their residue numbers.

For example:

open 2gbp
hide solvent
hbonds solvent restrict both reveal true
(among all solvent)

... or ...

hide solvent
hbonds solvent & ligand :<5 restrict both reveal true
(among solvent within 5 angstroms of ligand)

... or ...

hide solvent
hbonds /A:328,340-380,425 restrict both reveal true
(among water residues in chain A numbered 328, 340-380, 425)

See "hbonds" for what these options mean, and "command-line specification" for how to specify certain atoms, distance zones, etc.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/hbonds.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>

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




> On Jan 29, 2021, at 1:38 PM, Noor Agip <anaa2 at mrc-mbu.cam.ac.uk> wrote:
> 
> Hi,
> I am working on a membrane protein, and I am trying to map out water channels (responsible for proton conduction from one side of the membrane to another).  I am currently doing this manually from one connecting water molecule to the next using the structural analysis/H-bond function. Is there an easier way to do this with 14 linked water/residues? 
> Best wishes,
> Noor