VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 06 2003 - 10:52:52 CST

Hi Gemma,
  You can accomplish this one of several ways, here are a few
suggestions:
  1) Use VMD to manipulate the atom coordinates themselves, and
     write out a new PDB file with the modified coordinates.

     You can use the Mouse->Move->(Atom/Residue/Fragment/Molecule/Rep)
     mode to modify the orientation of atoms in VMD. This actually
     changes the atom coordinates. (Use shift key for rotations etc)

     Once you have things the way you want them, you can save the modified
     coordinates using an atomselect command, something like this:
     set sel [atomselect top "all"]
     $sel writepdb filename.pdb
     $sel delete

  2) If you prefer to do things using an orientation matrix, you can
     query the various viewing matrices in a manner similar to what
     the VMD save_state script does:

     proc save_viewpoint {} {
        global viewpoints
        if [info exists viewpoints] {unset viewpoints}
        # get the current matricies
        foreach mol [molinfo list] {
           set viewpoints($mol) [molinfo $mol get {
             center_matrix rotate_matrix scale_matrix global_matrix}]
        }
     }
     proc restore_viewpoint {} {
        global viewpoints
        foreach mol [molinfo list] {
           if [info exists viewpoints($mol)] {
              molinfo $mol set {center_matrix rotate_matrix scale_matrix
                global_matrix} $viewpoints($mol)
           }
        }
     }

You should be able to use these viewing matrices to do what you have
in mind, if you use them correctly. Note that this does not have any
effect on the atom coordinates, these are the matrices used for
viewing, so you'll have to use them to modify the coordinates in your
own script or in an external program, etc.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu
 
On Mon, Mar 03, 2003 at 02:39:51PM +0000, Gemma Kinsella wrote:
> Hi all,
>
> I wish to reorientate the position of my starting membrane protein so it will
> lie straighter in a bilayer for a molecular dynamics simulation. (i.e. loops
> at top and bottom)
>
> While I have no problem doing so visually, (vmd, sybyl) I have been unable to
> find a piece of software that will allow me to save the proteins new
> coordinates. I've been advised this can be achieved through calculating
> the transformation matrix used to reorient the protein with vmd. This same
> transformation matrix can then be applied to the original orientation within
> Amber. Does anyone have any insights as to how to go about this??? I am a
> little confused with the trans options and implimentations.
>
> Many thanks,
> Gemma 

-- 
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