[Chimera-users] H bonds

Elaine Meng meng at cgl.ucsf.edu
Mon Dec 31 17:31:12 PST 2018

Hi Kloe,
Both of these things I told you before.

(1) Chimera does not calculate stability values;  you have to use your own chemical intuition.

(2) The tutorial I recommended in the previous reply includes an example of calculating only the H-bonds to the ligand.


> On Dec 31, 2018, at 11:16 AM, kloe brathon <kloebrathon at yahoo.com> wrote:
> Hello,
>  Thank you for your reply!
> I tried that, but it gives me all the H bonds  of the structure and its a very complicated image. I was interested only in H bonds of ligands with its nearby residues. Maybe I should write any specificity on the script.
> Also, I am comparing the ligand bound and unbound form of two proteins. I used the Blast option that you had mentioned in a previous discussion. It worked perfectly to find a molecule that did not have the ligand, but now I am not sure on what can I do to compare their stabilities.
> I tried minimize option but it dd not give any difference to my protein.
> Regards,
> Kloe
> Happy New Year 2019!
> 30 Aralık 2018 Pazar 21:32:32 GMT+3 tarihinde, Elaine Meng <meng at cgl.ucsf.edu>şunu yazdı:
> Hi Kloe,
> I mentioned the FindHBond tool in my previous reply to you.  Did you try it?
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2018-December/015299.html>
> > Open tools from the Chimera Tools menu, for example:
> > 
> > Tools… Structure Analysis… FindHBond
> > Tools… Structure Analysis… Find Clashes/Contacts
> If you show a tool and click the Help button on that tool, it will explain the options.
> Also, you should go through the “Structure Analysis and Comparison” tutorial, which includes FIndHBond and some other things for looking at ligand-receptor interactions
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                      
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Dec 29, 2018, at 3:43 PM, kloe brathon <kloebrathon at yahoo.com> wrote:
> > 
> > Dear Chimera users,
> > I want to calculate H bonds between the ligand of my protein and its nearby residues. Could you give any suggestions on how to select this residues and calculate H bonds between them and the ligand?
> > Kind regards,
> > Kloe
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