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@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