[Chimera-users] creating a peptide bond between two fragments

Tim Travers tstravers at gmail.com
Tue Jun 7 19:07:24 PDT 2011

Hi Glenn,

You can combine the segments in Chimera into one PDB. What I usually do is
go to Favorites->Model Panel (which lists all the segments open in your
session), then there is a button on the right labeled 'copy/combine'. You
want the combine functionality.

Check the following for the Model Panel window:

there's a command-line version of 'combine' (which I haven't used
yet); details here:

Just to add, I would recommend minimizing the structure after combining the
segments. This can be done in Chimera with Tools->Structure
Structure. Also, besides checking the distance between the C and N atoms,
you would want to make sure they are in the trans configuration for peptide
In my limited experience, the minimization doesn't always fix peptide bonds
start in the cis configuration.

this helps,

On Tue, Jun 7, 2011 at 5:30 PM, Glenn Millhauser <glennm at ucsc.edu> wrote:

> Hi Folks,
>    I am trying to add a four amino acid segment to the N-terminus of a
> protein in the pdb.  I can generate the four residue stretch and move its
> C-term close to the N-term of the structured protein.  I can then select the
> C' and N atoms, which are about 1.0 Angstrom apart.  At that point, I am
> stuck.  Not sure how to add a bond and then create a proper structure.  I've
> played around with Join Models, but no luck.  Without a peptide bond
> recognized by Chimera, ribbons are discontinuous.  Any ideas?
> Many thanks,
> glenn
> Glenn L. Millhauser
> Department of Chemistry & Biochemistry
> UC Santa Cruz
> Santa Cruz, CA 95064
> 831 459 2176 voice
> 831 566 3337 cell
> 831 459 2935 fax
> 831 824 4645 google voice
> glennm at ucsc.edu
> http://chemistry.ucsc.edu/~glennm
> http://www.chemistry.ucsc.edu/faculty/millhauser.html
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