VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Jun 06 2007 - 09:24:18 CDT

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
> ----------------------------
>
>