From: Axel Kohlmeyer (
Date: Mon Jan 12 2009 - 09:05:41 CST

On Sun, 11 Jan 2009, Sebastian Stolzenberg wrote:

SS> Dear All,

dear sebastian,
SS> 1.)
SS> how does the math behind the VMD 4x4 transformation matrices work?
SS> ("" doesn't exist
SS> anymore)

there is a ton of text books that explain those, but probably the
best place to look for details are tutorials on rendering, where
similar 4x4 transformations are used as well. also, have you tried
searching wikipedia for information on transformation matrices?

SS> 2.)
SS> Eventually, I want to create a homo-two-protein-complex from one pdb file:
SS> - move a protein in VMD with the user-interface (rotate,translate by hand)
SS> - "Save State"->untitled.vmd
SS> - extract at the "viewpoints" parameters center_matrix,rotate_matrix,...
SS> - go back to VMD: "[atomselect top all] move $mytransformationsmatrix" to
SS> change the acutal pdb coordinates accordingly.

this will not work. those transformations will not change the
coordinates, only how you look at them. you have to create a
selection for the second molecule and then transform the coordinates
and save them.


SS> In particular, I do not know in what order I should apply/multiply the
SS> matrices
SS> center_matrix rotate_matrix scale_matrix global_matrix
SS> being given in my "untitled.vmd" file.

SS> Any help is much appreciated,
SS> Sebastian

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.