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

Elaine Meng meng at cgl.ucsf.edu
Mon Aug 26 11:44:54 PDT 2013

Hi Francesco,
Add bond is only for when the parts are already in the same model.  Join Models is for when they are in two separate models.

Join Models doesn't change the existing dihedrals.  It just joins the models using the distance and angle values you give it, which includes a new dihedral around the new bond.  I don't know what else to say other than to be careful to select the right atoms, as described, and enter the right values:

Also if you are joining peptides it should be easier to use the "C-N peptide bond" option, because then you don't have to add hydrogens and decide which to replace (as in the "other bond" option).

If you are sure it is changing some dihedral that you already have, you could use "Help… Report a Bug" and attach your session before the join (with atoms already selected).  In the report please describe all of the values you used in the join, and say which dihedral changes, and its value measured before and after the join.
I hope this helps,
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, 2013, at 11:32 AM, Francesco Pietra <chiendarret at gmail.com> wrote:

> 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>
> Hello;
> 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.
> thanks
> francesco pietra

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