From: Sebastian Stolzenberg (
Date: Mon Jan 12 2009 - 12:42:00 CST

Beautiful, thank you, Peter,

how about rotations, or is this only confined to translations?


Peter Freddolino wrote:
> Hi Sebastien,
> moving things by tcl commands actually have many charming qualities in
> terms of reproducibility and finer control. However, if you do want to
> move things with the mouse, you can make use of the various options
> under the Mouse->Move menu to move a molecule (these mouse modes
> actually do change the real coordinates) and then save its coordinates
> directly.
> Best,
> Peter
> Sebastian Stolzenberg wrote:
>> 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,
>> Sebastian