[Chimera-users] bond formation

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 26 10:38:06 PDT 2016


Hi Arthur,
If you just mean to draw a bond and not move anything, if the atoms are already selected you could just use command:  bond sel 
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html>

There is also a graphical interface, Tools… Structure Editing… Build Structure, the Adjust Bonds section.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#bond>

I hope this helps,
Elaine
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Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 26, 2016, at 7:14 AM, A G Szabo <agszabo at bell.net> wrote:

> I am working with a PDB file that has two proteins  docked together. As this is a model the two proteins do not have a bond between them. The model number  is the same for the two chains designated A and B. I have looked through the various tutorials, functions and tools to figure out how to actually place a bond between two residues that link the two chains. It is well established as to how the two proteins would be linked if the bond had been formed.
> The linkage is between the S of a  Cysteine and carbonyl carbon at the C-terminal of the other  protein.
> I think  I have managed to select both atoms, but cannot determine how  to include a bond.
> Your assistance is appreciated.
> Arthur Szabo




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