VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Oct 31 2007 - 17:25:50 CDT

Hi,
  Have you gone through any of the VMD/NAMD tutorials? If you know
the transformation you want to apply to the protein, you can use
atom selections and '$sel move' commands and their many variants, to
perform rotations, translations, and other operations on the structure.
The NAMD structure building tutorials should have more useful examples on
this specific type of work, even though much of the building is done
within VMD:
  http://www.ks.uiuc.edu/Training/Tutorials/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Oct 31, 2007 at 07:14:12PM +0100, maria goranovic wrote:
> CORRECTION:
>
> the protein does not need to be "aligned along the bilayer normal", it just
> needs to be inserted into the membrane, and its orientation in the protein
> is determined by the angle between the bilayer normal and the axis of one of
> its helices (the angle is 30 degrees)
>
> Sorry if this was not clear the first time
>
> -maria
>
>
> On 10/31/07, maria goranovic <mariagoranovic_at_gmail.com> wrote:
> >
> > Hi
> >
> > I have a multi-segment protein which needs to be aligned along the bilayer
> > normal. I have information about the angle between the bilayer normal and
> > one of the helices of the protein. Once I have the principal axes of the
> > protein aligned with the coordinates axes, how can I go about using the
> > angle information to reorient the protein in the membrane ?
> >
> > Thanks a million for the suggestions,
> >
> > -Maria
> >
> > --
> > Maria G.
> > Technical University of Denmark
> > Copenhagen
> >
>
>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078