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

Francesco Pietra chiendarret at gmail.com
Tue Aug 27 01:47:24 PDT 2013

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret at gmail.com>
Date: Tue, Aug 27, 2013 at 10:45 AM
Subject: Re: [Chimera-users] Fwd: Make bonds in a large polypeptide
To: UCSF Chimera Mailing List <chimera-users at cgl.ucsf.edu>

Hi Elaine:

Matching was very good by using MultiSeq plugin of VMD.

The situation before "Join Models" is represented by the couple of strands
on the left. Following "Join Models", by the couple of strands at the
right. Highlighted in red Ala-Leu before bonding and after bonding. That
was done with distances and dihedrals as in the integer subunit from which
they come. In my hands, formation of a regular alpha-helix could improve a
little on playing with distance/dihedral values, but only little.

Putting both fragments as a single model, command "make bond' between NH of
Leu and CO of Ala refused to work. Therefore, I asked whether 450 residues
are too much (for example, they are too much for Molefacture in VMD).

As "Join Models" is certainly a proved tool, I am not submitting any bug.
There must be something wrong either with files or doing.  Looking for

Thanks a lot for your interest.


On Mon, Aug 26, 2013 at 8:44 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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:
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join
> >
> 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
> ----------
> 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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