[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:

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):

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)
(B) PseudoBond Reader

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:

I hope this helps,
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.

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