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@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.