From: Sebastian Stolzenberg (
Date: Sun Jan 11 2009 - 22:58:47 CST

Dear All,

how does the math behind the VMD 4x4 transformation matrices work?
("" doesn't
exist anymore)

Eventually, I want to create a homo-two-protein-complex from one pdb file:

- move a protein in VMD with the user-interface (rotate,translate by hand)
- "Save State"->untitled.vmd
- extract at the "viewpoints" parameters center_matrix,rotate_matrix,...
- go back to VMD: "[atomselect top all] move $mytransformationsmatrix"
to change the acutal pdb coordinates accordingly.

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

Any help is much appreciated,