mapping out water channels in chimerax
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
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@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
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@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@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
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@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@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@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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participants (2)
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Elaine Meng -
Noor Agip