[chimerax-users] mapping out water channels in chimerax

[Noor Agip]

Hi Elaine,

There are both internal and external water molecules. I will try to restrict the selection to water molecules near the protein of interest. Thank you Elaine. I will try your suggestion.

Best wishes,
Noor


> On 29 Jan 2021, at 21:52, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> 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
>