From: Axel Kohlmeyer (
Date: Mon Jan 12 2009 - 14:32:27 CST

On Mon, 12 Jan 2009, Sebastian Stolzenberg wrote:

SS> Being able to move a protein A by "drag-and-drop" with respect to another
SS> fixed protein B is a wonderful, intuitive VMD tool. It would be great, if I

actually, i agree with peter and would consider this rather crude
and unreliable, particularly if you don't have a proper stereo screen.

you should seriously try to do this via script (with tkcon even
interactive operations are convenient). if you have a proper .pdb
file, then the required symmetry operations should already be specified
somewhere in the header or in the literature describing it and building
the transformation matrix is straightforward. if it is a homodimer, you
probably just need to define the proper center and then do some 90
degree rotations (which mean that you have only 0 and +/-1 in your
rotation matrix).

SS> could also somehow make the changes I "see" on the screen in A to last as
SS> changed pdb coordinates as well. So there is really no way I can convert the
SS> transformation matrices for changing viewpoints into transformation matrices
SS> for changing the actual coordinates?
SS> Is there another way I could make this "drag-and-drop"TO"pdb coordinates"
SS> conversion, or will I have to tediously move my protein A with tcl console
SS> commands?

hehe. it is tedious only because it seems unfamiliar to you.
please give it a try and you'll see that it can be pretty
nice and at some point even addictive. looking at some of the
scripts i wrote for VMD, i occasionally wonder how i could
ever have managed without.


SS> Thank you so much,
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.