[Chimera-users] Regarding Hydrogen Bond

[Amit Jaiswal]

Dear Elaine,
                 I am stuck with a new problem and that is can I select
multiple
residues from different chains and check their interaction. There are some
results from  Haddock and I want to study the interaction residues from
different chains. Is it also possible to know their bonding pattern? Please
help me out.

On Thu, Oct 25, 2012 at 9:53 AM, Amit Jaiswal <amitjai20 at gmail.com> wrote:

> Dear Elaine,
>
>                   Thanks for your mail and suggestions. I will post
> questions
> 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,
> Pondicherry,
> India.
>
>
> 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.
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~
>
>


-- 

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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