[Chimera-users] bond formation
A G Szabo
agszabo at bell.net
Fri Aug 26 11:33:34 PDT 2016
Thanks for the tips but not successful. I checked some of the help sections,
like select and atom specifier, and tried the command below
Bond sel :88A at SG:96B at CA
Mangled atom specifier!
I tried the suggestion of using the Tools menu, but not evident how to do
Is there a way to select more than one atom using cntrl and the mouse arrow.
From: Elaine Meng [mailto:meng at cgl.ucsf.edu]
Sent: August-26-16 1:38 PM
To: A G Szabo
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] bond formation
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
There is also a graphical interface, Tools. Structure Editing. Build
Structure, the Adjust Bonds section.
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 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
> 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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