[Chimera-users] H bonds

kloe brathon kloebrathon at yahoo.com
Mon Dec 31 11:16:44 PST 2018

 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.
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?


> 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


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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