VMD-L Mailing List

From: Marc Baaden (baaden_at_smplinux.de)
Date: Wed Oct 30 2002 - 11:52:09 CST

Hi John,

thanks for your suggestions.
I had a look at the various things you suggested. In the end I did a
coordinate transformation, but without a fit to another structure, just
using VMD commands to define the transformation matrices. The (experimental)
code I am currently using is attached below.

Thanks,
Marc

johns_at_ks.uiuc.edu said:
>> Hi Marc,
>> I still think that using (well, abusing in this case :-) the
>> best-fit code in VMD is the easiest way to do what you need: Rather
>> than fit the whole structure, just fit 3 atoms of interest, just as
>> you say, something in the center, some residue X pointing out of the
>> screen, and some residue Y pointing in another consistent direction.
>> You'll need at least 3 atoms to come up with correction matrix to
>> bring the other structures into the same viewing orientation. [..]

The little code snippet below uses the geom_center routine from the VMD
user manual. You invoke it with something like

position_view "protein and name CA" "protein and resid 714"

# POSITION_VIEW
# center on the geometrical center of the specified selection, and orient the
# central axes -> $rot_sel vector along the x axis
#
proc position_view { cen_sel rot_sel } {
  # Move protein center to 0 0 0
  set sel [atomselect top $cen_sel]
  set cen [geom_center $sel]
  set mat [ trans origin $cen ]
  set move_sel [atomselect top "all"]
  $move_sel move $mat

  # Orient protein
  set sel [atomselect top $rot_sel]
  set cen [geom_center $sel]
  set tmpx [ vecdot $cen { 1 0 0 } ]
  set tmpy [ vecdot $cen { 0 1 0 } ]
  set vec " [list $tmpx] [list $tmpy] 0 "
  set mat [ transvecinv $vec ]
  $move_sel move $mat
} 

-- 
 Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
 mailto:baaden_at_smplinux.de  - ICQ# 11466242 -  http://www.marc-baaden.de
 FAX/Voice +49 697912 39550  -  Tel: +44 1865 275380  or  +33 609 843217