[Chimera-users] electrostatic interactions

[Ruchika]

Hi Elaine
Thanks for the confirmation !! I tried looking into these details, however, I still wanted to confirm with you. Thanks again !!
I have another question. I do understand that I can mutate a residue to the different one using the rotamer tool. I am just wondering if I would like to make an insertion or deletion mutation in the protein, are there any available tools in the chimera. Please let me know.
Thanks !!
Regards
Ruchika
________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Tuesday, September 22, 2020 8:57 AM
To: Ruchika <Ruchika at ucsf.edu>
Cc: Chimera <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] electrostatic interactions

Hi Ruchika,
H-bonds include salt bridge interactions.  That is, many H-bonds are salt bridges, and biomolecular (e.g. protein-protein) salt bridges are generally H-bonds.   See the FindHBonds page for a description of what atom types it considers:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html#criteria>
Regards
Elaine

> On Sep 21, 2020, at 9:27 PM, Ruchika <Ruchika at ucsf.edu> wrote:
>
> Hi Elaine, thanks for your response !! I am just wondering if this Find H-bond tool can also find any other polar interactions than Hydrogen bonds, like salt bridges. Please let me know. Thanks !!
> Regards
> Ruchika
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sent: Saturday, September 19, 2020 9:18 AM
> To: Ruchika <Ruchika at ucsf.edu>
> Cc: Chimera <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] electrostatic interactions
>
> Hi Ruchika,
> There is a FindHBond tool, and also coloring the surface by electrostatic potential.
>
> Of course you can just look at the help pages for all the tools or commands you are interested in.  The list of all tools has links to their individual help pages:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecontrib.html>
>
> ... but I recommend going through these tutorials for examples of using them:
>
> (1) Structure Analysis and Comparison
>      (includes Find Contacts, FindHBond, surface coloring by hydrophobicity)
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>
>
> (2) Image Tutorial: Surface Properties
>     (surface coloring by hydrophobicity and electrostatic potential)
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.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 Sep 18, 2020, at 5:57 PM, Ruchika <Ruchika at ucsf.edu> wrote:
> >
> > Hi Elaine
> > I do see "Find out clashes and contacts" feature in Chimera. I am wondering if there is any feature which can check on electrostatic interactions as well. Please let me know.
> > Thanks !!
> > Regards
> > Ruchika
>
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