[chimerax-users] mapping out water channels in chimerax

[Elaine Meng]

In that case, could be something like

hbonds solvent & protein :<4.2 restrict both reveal true
 
... for a 4.2-angstrom cutoff from any protein.  Use any cutoff you like, of course. :-)

Elaine

> On Jan 29, 2021, at 2:08 PM, Noor Agip <anaa2 at mrc-mbu.cam.ac.uk> wrote:
> 
> 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
>> 
> 
> 
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