[Chimera-users] Regarding Hydrogen Bond

Elaine Meng meng at cgl.ucsf.edu
Wed Oct 24 09:33:38 PDT 2012


Dear Amit,
You can identify hydrogen bonds with FindHBond (in menu under Tools... Structure Analysis).  Click the Help button on that tool or see here for instructions:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html>

If you want to analyze the environment around the metal and then add metal coordination bonds, you could use Metal Geometry (in menu under Tools... Structure Analysis):
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/metalgeom/metalgeom.html>

If you don't care about analysis and just want to draw a line between two atoms, you could do that using either of the following:
(A) distance measurements, for example using the Distances tool (change label to "none" if you don't want to see the distance value)
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances>
(B) PseudoBond Reader
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.html>

Please send Chimera questions to the chimera-users at cgl.ucsf.edu address so that everybody can benefit.  

You can search the manual using Help... Search Documentation in the Chimera menu, and you can search the chimera-users messages here:
<http://www.cgl.ucsf.edu/chimera/docs/feedback.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 24, 2012, at 8:54 AM, Amit Jaiswal wrote:

> Dear Dr.Meng,
>   Many thanks for your mail and suggestion for Metal fixation. I have done what you have advised. So, now my metal is near the catalytic site. So the next step is  to form bond between Mg and Aspartic Acid residues. Now, I am confused. So I want to ask weather hydrogen bond and co-ordinate bond can be formed in Chimera?
> Please do let me know.
> 




More information about the Chimera-users mailing list