VMD-L Mailing List

From: Himanshu Khandelia (hkhandel_at_memphys.sdu.dk)
Date: Wed Jun 06 2007 - 10:02:54 CDT

I want to confine the changes only to the residues in question (so that
only the structure of the loop changes, and not that of the rest of the
structure). I was doing this using:

for {set i 22 } { $i < 26 } { incr i } {
set sel [atomselect top "resid $i and name CA"]
$sel set phi -60
$sel set psi -45
}

So the {phi,psi} pair of only residues 22 through 26 changed. But the
entire molecule downstream rotates because of the changes enforced on the
dihedral angles of residues 22-25. I hope its clearer now ?

Thank you,

-himanshu

----------------------------
Himanshu Khandelia, PhD
Research Assistant Professor (Postdoc)
MEMPHYS, Center for Membrane Physics: www.memphys.sdu.dk
-----------------------------

On Wed, 6 Jun 2007, Peter Freddolino wrote:

> Hi Himanshu,
> I think I may not understand exactly what you're after -- do you want to
> rotate one entire helix about the dihedral angle, or confine your
> changes only to the residue under consideration? In either case the
> answer is more or less the same: make a selection containing the atoms
> you want to move and use the "trans bond" command
> (http://www.ks.uiuc.edu/Research/vmd/current/ug/node178.html) with the
> coordinates of the atoms at either end of the bond to set up a
> transformation matrix to apply to the selected atoms.
> Best,
> Peter
>
> Himanshu Khandelia wrote:
> > Hi,
> >
> > My protein consists of two transmembrane helices connected by a
> > periplasmic loop. I want to artificially extend one of the helices into
> > the loop region. One way to do this is to alter the dihedral angles of the
> > relevant amino acid residues. However, changing the (phi,psi) values of
> > some of the loop residues to helix specifications (-60,-45) will distort
> > the topology of the protein downstream of the altered region. Does someone
> > know of a way to alter dihedral angles of ONLY the specific region of the
> > protein, while keeping the positions of the rest of the atoms constant ?
> > Any other suggestions?
> >
> > Thank you for the help,
> >
> > ----------------------------
> > Himanshu Khandelia, PhD
> > MEMPHYS, Center for Membrane Physics: www.memphys.sdu.dk
> > ----------------------------
> >
> >
>