[Chimera-users] translation and rotation in MATLAB using transformation matrices from chimera

Elaine Meng meng at cgl.ucsf.edu
Mon Apr 24 09:44:43 PDT 2017


Dear Oleksiy,
I can’t advise on MATLAB, just wanted to point out that in Chimera, after fitting you could resample one map “A" on the grid of another “B".  This would create a new resampled map “C” (although with some loss of resolution due to interpolation) that is already in register with “B” so you wouldn’t have to specify a transformation.

The command is “vop resample”:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#resample>
See also:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting>

Best,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 24, 2017, at 9:30 AM, Oleksiy Kovtun <okovtun at mrc-lmb.cam.ac.uk> wrote:
> 
> Dear all, 
> I need to merge two maps in MATLAB using
> alignment data from chimera. Inputs:  two maps of the same box size, origin. I use matrixget -  to report translation and rotation
> matrices for the aligned map . Translation operation works well when transferred into MATLAB (briefly, translation matrix gets converted in eulers and pased on to tom_rotate command in MATLAB, TOM package). However the x y z translation coordinates (the fourth column top to bottom in matrixget - output) are way off the real translation when using tom_shift command in MATLAB, TOM.
> I found out that if I open the rotated map
> and fit it again, it gives close to correct translation
> matrix.
>  
> What's going wrong here? Does anyone have a
> solution how to overlay 3D arrays in MATLAB using chimera-reported transformation matrices?
>  
> Many
> thanks,
> Oleksiy 




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