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 current
session), then there is a button on the right labeled 'copy/combine'. You would
want the combine functionality.
Check the following for the Model Panel window:
Alternatively, 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 Editing->Minimize
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 bonds.
In my limited experience, the minimization doesn't always fix peptide bonds that
start in the cis configuration.
Tim
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
_______________________________________________
Chimera-users mailing list
Chimera-users@cgl.ucsf.edu
http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users