rotation parameters of the map
Dear colleagues, When I align one map to the other (either manually or by using the Fit option), I would like to know the applied rotation parameters. How to find them our when a) using just Fit option b) rotation manually and then using the Fit option? Thank you Sincerely, Dmitry
Hi Dmitry, The fitmap command or clicking Fit on the dialog already reports in the Log the rotation it performs (e.g. difference in angle before and after the fit). <https://rbvi.ucsf.edu/chimerax/docs/user/commands/fitmap.html> I tested this by making two maps from similar atoms, rotating one 30 degrees with the "turn" command, and then using "fitmap" to fit them (which reversed my rotation) and reported: =-=-= Log contents =-=-= Fit map 2gbp map 5 in map 2gbp map 5 using 1242 points correlation = 0.8771, correlation about mean = 0.6952, overlap = 35.83 steps = 84, shift = 0.773, angle = 30 degrees Position of 2gbp map 5 (#3) relative to 2gbp map 5 (#2) coordinates: Matrix rotation and translation 0.99998977 0.00451511 0.00026156 -0.22015058 -0.00451493 0.99998959 -0.00066558 0.20896484 -0.00026456 0.00066439 0.99999974 -0.13784757 Axis 0.14546994 0.05754589 -0.98768769 Axis point 44.68129671 52.60203567 0.00000000 Rotation angle (degrees) 0.26191737 Shift along axis 0.11615012 =-=-= See the "angle = 30 degrees" part. It does not include any hand movements that you did, if that's what you meant. To get the overall transformation of one model relative to another including hand movements and fitting, after doing all that stuff, you could use command "measure rotation" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation> 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 13, 2021, at 9:15 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear colleagues,
When I align one map to the other (either manually or by using the Fit option), I would like to know the applied rotation parameters.
How to find them our when
a) using just Fit option b) rotation manually and then using the Fit option?
Thank you
Sincerely,
Dmitry
Dear Elaine, Thank you! Sincerely, Dmitry
On 13. Dec 2021, at 18:31, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Dmitry, The fitmap command or clicking Fit on the dialog already reports in the Log the rotation it performs (e.g. difference in angle before and after the fit). <https://rbvi.ucsf.edu/chimerax/docs/user/commands/fitmap.html>
I tested this by making two maps from similar atoms, rotating one 30 degrees with the "turn" command, and then using "fitmap" to fit them (which reversed my rotation) and reported:
=-=-= Log contents =-=-= Fit map 2gbp map 5 in map 2gbp map 5 using 1242 points correlation = 0.8771, correlation about mean = 0.6952, overlap = 35.83 steps = 84, shift = 0.773, angle = 30 degrees
Position of 2gbp map 5 (#3) relative to 2gbp map 5 (#2) coordinates: Matrix rotation and translation 0.99998977 0.00451511 0.00026156 -0.22015058 -0.00451493 0.99998959 -0.00066558 0.20896484 -0.00026456 0.00066439 0.99999974 -0.13784757 Axis 0.14546994 0.05754589 -0.98768769 Axis point 44.68129671 52.60203567 0.00000000 Rotation angle (degrees) 0.26191737 Shift along axis 0.11615012 =-=-=
See the "angle = 30 degrees" part.
It does not include any hand movements that you did, if that's what you meant. To get the overall transformation of one model relative to another including hand movements and fitting, after doing all that stuff, you could use command "measure rotation" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation>
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 13, 2021, at 9:15 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear colleagues,
When I align one map to the other (either manually or by using the Fit option), I would like to know the applied rotation parameters.
How to find them our when
a) using just Fit option b) rotation manually and then using the Fit option?
Thank you
Sincerely,
Dmitry
participants (2)
-
Dmitry Semchonok -
Elaine Meng