[Chimera-users] How to place two identical proteins "near" each other

[Elaine Meng]

Hi Marla,
Actually Chimera’s “tile” is not just a tile view, it actually puts structures in separate locations.  

However, one can of course move a structure without moving the others.  You can “freeze” any structure so that it ignores mouse manipulations, by deactivating it (for example, unchecking the “A” button in Model Panel opened from Favorites menu).
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>

For more precise operations, you can specify in commands which models to move.  See the commands “move” (translation),  “turn” (rotation), etc. with the “models” option.  For example, to get side-by-side comparisons, I first superimpose the models so that they’ll be in a certain orientation and then translate them apart:

move x -20 mod #0
move x 20 mod #1

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/move.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jul 20, 2018, at 10:25 AM, Marla DeKlotz <mdeklotz at gmail.com> wrote:
> 
> I am trying to prepare a pdb to use in Rosetta docking.  I need to place two copies of the same protein "near" each other, in roughly the alignment they should have after they dock together.  Chimera seems to always overlay the two copies and I can't figure out a way to separate them and move/rotate each one independently.  I don't want a tile view, I need them to have a real relationship in space so Rosetta knows where to "aim" its docking protocol.
> 
> Thanks,
> Marla