[Chimera-users] User defined h bonds

Elaine Meng meng at cgl.ucsf.edu
Thu Jun 10 13:27:31 PDT 2010

Dear S,
You can draw any atom-atom lines ("pseudobonds") you want, by creating a text file that lists the pairs of atoms and then reading that file in using PseudoBond Reader (under Tools... Depiction).  Colors and labels can also be given in the file.  PseudBond Reader and the file format are described here:


After you create the pseudobonds, you can change other things about their appearance (line width, line style, ... ) using "attributes" in PseudoBond Panel (under Tools... General Controls), or individually by selecting a pseudobond and then using the Selection Inspector, or with the command "setattr".


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 Jun 10, 2010, at 11:26 AM, snoze pa wrote:

> Dear Chimera Users,
> Manually How can I show hbonds in  chimera. Suppose I want to h bonds
> between residue 65 NH and 80 O. and show them using red or blue color.
> Is it possible to read this information from a file so that I can
> read all hbonds information in one run.
> Thank you
> S

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