[Chimera-users] Fwd: Make bonds in a large polypeptide

Francesco Pietra chiendarret at gmail.com
Mon Aug 26 11:32:38 PDT 2013

Must add that I had also tried "Join Models" at no avail. Restraing
concerned dihedrals, through tmsd-colvars applied to the CA atom, so that
the side chains could move. With "Join Models" I was  therefore unable to
get the continuous alpha helix shape: formation of the new peptide bond
resulted in a kinked alpha helix, no matter how I dealt with the "Join
Models" entries. What I need is that the new peptide bond is formed without
altering the dihedrals based on the CA atoms.

francesco pietra

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret at gmail.com>
Date: Mon, Aug 26, 2013 at 8:02 PM
Subject: Make bonds in a large polypeptide
To: chimera <chimera-users at cgl.ucsf.edu>

Is there a limit in the number of atoms when using the function "make a
bond"? I was trying that in a polypeptide of 450 standard residues (I made
it a single model) and it did not work.

Just to not be cryptic, that need arises from having modeled by special
techniques the initial portion of the polypeptide. Now I would like to
replace that portion with the modeled one. I had restrained with
rmsd-colvars the dihedrals of a short stretch of alpha helix, so that I
could align the modeled portion with the polypeptide.

francesco pietra
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