Hi Nikita, Well, it may not be a very clean result if you positioned the structures by hand, but you could try the following: (1) save one subunit to PDB relative to the other (or alternatively, transformed coordinates of both subunits) so that when you close everything and reopen the two, they are already in the correct relationship to one another without your moving them separately <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html> (2) after closing the original and reopening what you'd saved, superimpose the subunits, for example with matchmaker <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html> (3) use “measure rotation” to see what transformation was required to superimpose the two <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation> For example, I made an artificial example by opening two copies of the same protein and translating one copy along Y and rotating it around Y, and then doing the other steps as described above, commands: open 2mnr open 2mnr move y 50 mod #1 turn y 50 mod #1 focus write relative 0 1 ~/Desktop/test.pdb close session open 2mnr open ~/Desktop/test.pdb mm #0 #1 measure rotation #0 #1 … then the Reply Log gave this, correctly reporting the 50-degree rotation and 50-angstrom shift: Position of test.pdb (#1) relative to 2mnr (#0) coordinates: Matrix rotation and translation 0.64278724 0.00000180 -0.76604476 21.79174905 -0.00000192 1.00000000 0.00000073 -49.99995244 0.76604476 0.00000100 0.64278724 -18.97185024 Axis 0.00000018 -1.00000000 -0.00000243 Axis point 31.23835900 0.00000000 13.88038965 Rotation angle (degrees) 50.00002797 Shift along axis 50.00000235 However, if you positioned by hand, the axis of rotation won’t be exactly the same as the direction of translation, so the result may not be so clear. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 17, 2018, at 2:01 PM, Nikita Chopra <chopranikita.2@gmail.com> wrote:
Hi I have two protein subunits, which I have aligned along the z-axis. I am considering both the subunits as rigid bodies. Is there a way I could find the screw transformation (rotation along z-axis and displacement along xy plane) between them in chimera ? Thank you for your help.