From: Sebastian Stolzenberg (
Date: Mon Jan 12 2009 - 12:09:50 CST

Thank you for your quick reply, Axel,
> SS> 2.)
> SS> Eventually, I want to create a homo-two-protein-complex from one pdb file:
> SS>
> 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.
Being able to move a protein A by "drag-and-drop" with respect to
another fixed protein B is a wonderful, intuitive VMD tool. It would be
great, if I could also somehow make the changes I "see" on the screen in
A to last as changed pdb coordinates as well. So there is really no way
I can convert the transformation matrices for changing viewpoints into
transformation matrices for changing the actual coordinates?

Is there another way I could make this "drag-and-drop"TO"pdb
coordinates" conversion, or will I have to tediously move my protein A
with tcl console commands?

Thank you so much,