[Chimera-users] coordinate rotation measuring

Tom Goddard goddard at sonic.net
Mon Jun 6 12:10:15 PDT 2011

Hi Jeffrey,

   The "measure rotation" command determines the rotation between the 
coordinate frames of two models that have been moved relative to one 
another.  A rigid motion involves a rotation and a translation.  The 
rotation axis direction and angle is uniquely determined (for rotation 
angles > 0) but the axis could go through any point in space.  Using 
axes that go through different points just changes the translation 
needed to achieve the rigid motion.  There is a point you can choose the 
rotation axis to go through such that the translation needed is only 
parallel the rotation axis.  Basically the rigid motion consists of a 
rotation about this axis, and a translation parallel to that axis.  That 
is the rotation axis placement given by "measure rotation".  It does not 
allow you to place the axis wherever you want.

   There is currently no option in the measure rotation command to make 
the slab display larger.  You can edit a Python file


changing the lines near the end

     e = 2       # Factor for enlarging square
     dz = chimera.cross(axis, sq1) * .05 # Thickness vector

to say

      e = 4
      dz = chimera.cross(axis, sq1) * .1

to make the slabs bigger.

   I'll add a feature request to improve the measure rotation command to 
include slab size options.


> Hi,
> I'm currently working on a gp140 model and have docked coordinates for 
> 2 different conformations. I am trying to measure the rotation between 
> the docked coordinates using the method in the EM-fit tutorial and i 
> had a few questions.
> How does the "measure rotation #1 #3 showslab true" command measure 
> the rotation? How does it determine the axis of rotation? Is it 
> possible for me to create my own axis? Is there any way to increase 
> the size of the slabs (they are too small visually)?
> -Thanks!

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