[Chimera-users] Regarding Hydrogen Bond

Amit Jaiswal amitjai20 at gmail.com
Wed Oct 24 21:23:20 PDT 2012

Dear Elaine,

                  Thanks for your mail and suggestions. I will post
on chimera-users at cgl.ucsf.edu from next time on wards. I will try the tips
and thus report you if problem persists.

With kind regards,
Amit Jaiswal,
Pondicherry  University,

On Wed, Oct 24, 2012 at 10:03 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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.
> >


Yours Sincerely,

Amit Jaiswal,
Department of Bioinformatics,
School of Life Sciences,
Pondicherry Central University,
Kalapet, Pondicherry,
Puducherry - 605 014.
Phone No.: +91 8124954834.

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