VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Jan 12 2009 - 19:30:51 CST

Try holding shift or middle-clicking while moving the molecule.
See http://www.ks.uiuc.edu/Research/vmd/current/ug/node28.html for more
documentation on these modes.
Best,
Peter

Sebastian Stolzenberg wrote:
> Beautiful, thank you, Peter,
>
> how about rotations, or is this only confined to translations?
>
> Cheers,
> Sebastian
>
> 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
>>>
>>>