[Chimera-users] Measure relative orientation of molecules

Tom Goddard goddard at sonic.net
Tue Jan 10 15:31:45 PST 2012

> Hi,
>   It is not obvious to me if there is a simple way to do this in 
> Chimera. Given a PDB file containing a number of chains of identical 
> molecules arranged into a helix, but without exact helical symmetry, 
> is there some way to measure the rotation between adjacent chains? I 
> imagine that I can use MatchMaker, and then convert the resulting 
> rotation matrix to the angle about the helical axis...
> Regards,
> Ed

Hi Ed,

   If PDB models #1 and #2 are fit to a filament map you can use Chimera 

     measure rotation #1 #2

which will produce output in the Reply Log (menu Favorites / Reply Log) like

Position of 1mwk (#2) relative to 1mwk (#1) coordinates:
   Matrix rotation and translation
      0.89907669  -0.42653054  -0.09865501 -14.80260678
      0.38452015   0.87709721  -0.28782762   9.59677669
      0.20929731   0.22084426   0.95258724 -47.13790770
   Axis   0.50580078  -0.30621414   0.80647286
   Axis point  19.41814624  18.14474471  -0.00000000
   Rotation angle (degrees)  30.18795070
   Shift along axis -48.44128198

This specifies the rotation in PDB #1 coordinates, not the coordinates 
of the map these two molecules have been fit into.  It is described as a 
3x3 rotation matrix and a translation (4th column of above matrix).  And 
it is equivalently described as an axis, point on the axis, rotation 
angle and shift along the axis.  The command will also show in the 
graphics window the axis of rotation for this latter specification.

Unfortunately there is not an option to express this rotation in the map 
coordinate system which is probably what you are interested in.  Here's 
a way to do that though.  Fit the first molecule in the map.  Then write 
out that PDB file using the map coordinates using Chimera menu File / 
Save PDB... with the "Relative to model mymap.mrc" option enabled.  Now 
close that fit molecule and open the saved PDB.  It has the same 
coordinate system as the map.  Open a second copy of that PDB and fit it 
in another position in the map.  Then use the "measure rotation #1 #2" 
command (can be shortened to "me rot #1 #2").

I'll see if I can easily add an option to the measure rotation command 
to report the result in the map coordinate system.


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