[Chimera-users] bond formation

A G Szabo agszabo at bell.net
Fri Aug 26 11:33:34 PDT 2016


Elaine

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

Msg received

Mangled atom specifier!

I tried the suggestion of using the Tools menu, but not evident how to do
it.

Is there a way to select more than one atom using cntrl and the mouse arrow.

Thanks

arthur

-----Original Message-----
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

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.h
tml#bond>

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 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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