[Chimera-users] bond formation

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 26 12:09:01 PDT 2016

Hi Arthur,
The whole command is “bond sel” if the two atoms are selected, you don’t need the atom specifiers!  Or, if they are not selected, then omit the “sel” and give the atom specifiers instead.  Also, your atom specifiers are messed up, there should be a dot (.) before the chain ID, and the carbonyl carbon is named C, not CA, e.g.

bond :88.a at sg:96.b at c

(capitalizing the chain and atom names is optional)

To select two atoms, Ctrl-click the first one and then Shift-Ctrl-click the second one.  How to select with the mouse is explained here:


On Aug 26, 2016, at 11:33 AM, A G Szabo <agszabo at bell.net> wrote:

> 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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