[Chimera-users] Calculating screw transformation between two protein subunits

[Elaine Meng]

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 at 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.
>