[Chimera-users] Translate onto the X-axis

[Elaine Meng]

Hi Yasser,
It's a little undefined since I'm not sure whether you mean screen X-axis, which is always horizontal, or X in the coordinate system of some data, which could be pointing in any direction if you have rotated that data.  Also unclear whether whether your two proteins are in the same coordinate system as each other.

For the first case, if you just want a side-by-side view of similar proteins, how I do this is to superimpose the proteins with matchmaker (or whatever method works best for your case), then manually rotate to the orientation I want, then use "move x" commands specifying one model or the other ("models" option)  to move them apart horizontally to left and right in the coordinate system of the screen.
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/move.html>

For the second case, along X axis in the coordinate system of the data (but assuming the proteins are in the same coordinate system as each other), I would just use "measure center" 
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#center>

...to report the current coordinates of the center of mass of each one, and then use "move x" "move y" and "move z" commands with the "models" option to translate each one, plus "coordinateSystem #1" option if using the coordinate system of model 1, to put that model's center of mass at the desired point.  E.g. if center of mass is initially reported as 1,1,5 and you want it at 0,0,0 you would move that model -1 in X, -1 in Y, -5 in Z.

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


> On Dec 14, 2021, at 12:39 AM, Yasser Almeida via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hello,
> 
> I have a complex of two proteins that I want to align to the X-axis. Specifically, I want to define a vector between the COMs of each protein, and then translate the whole system so that the vector is on the X-axis, where the COM of one protein is on the cartesian origin [0, 0, 0] and the other COM is in [+X, 0, 0].
> 
> How can I achieve this with Chimera?
> 
> Thanks in advance,
> Yasser