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@gmail.com> wrote:
Dear Elaine,
Thanks for your mail and suggestions. I will post questions on chimera-users@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@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...
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...
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/struc...
(B) PseudoBond Reader < http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.h...
Please send Chimera questions to the chimera-users@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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-- Yours Sincerely, ~~~~~~~~~~~~~~~~~~~~~~~~ Amit Jaiswal, Department of Bioinformatics, School of Life Sciences, Pondicherry Central University, Kalapet, Pondicherry, Puducherry - 605 014. Phone No.: +91 8124954834. ~~~~~~~~~~~~~~~~~~~~~~~~~