[chimerax-users] Move model from position

[Elaine Meng]

Dear Lara,
If I understand correctly, it is not necessary to use such an elaborate procedure or to save a positions file.  Instead you could just use the "view position" command to apply the rotation/translation of one model to another model, something like:

view position #3 sameas #2

See:
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#position>

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

> On Dec 9, 2020, at 10:48 AM, Lara Koehler <lara.koehler at universite-paris-saclay.fr> wrote:
> 
> Dear chimeras users and developers,
> 
> I would like to translate and rotate a model according to the rotation and translation matrix given by a fitmap. More precisely :  I fit model #2 in map #1 and save the corresponding translation and rotation matrix with the save command. Then, I want to turn and move a model #3 so that it has the same position and rotation as model #2 (each correspond to the same pdb file). However, I want to do this automatically, so I need to do it from the matrix that is saved in a .positions file, and not from the (axis, axis point, rotation angle and shift along axis) values given by fitmap, but from the Matrix rotation and translation values. So far,
> - I compute the axis of rotation and the angle from the rotation matrix given by fitmap models #2 inMap #1
> - I turn #3 around this axis and angle, in coordinateSystems #1
> - I apply the translation also measured by fitmap models #2 inMap #1 to #3 (with three calls of the move command, for each axis x,y,z)
> However, there is a small gap between model #2 and model #3, whereas both should be at the exact same position. 
> 
> Maybe this has to do with the rotation center that is used in fitMap, but it cannot be saved in a .positions file, and I don't know how to recover it from the matrix rotation and translation given by fitmap. Do you have any idea of what I'm doing wrong, or how I could place model #3 at the same exact position as model #2 from the .positions file of model #2, and by moving and rotating model #3 ? (What I want to do then is re-apply this same transformation to build a chain of the same protein)
> Thanks,
> Lar