VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Jan 12 2009 - 12:17:53 CST

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
>