[Chimera-users] coordinate rotation measuring
goddard at sonic.net
Mon Jun 6 12:10:15 PDT 2011
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
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.
> 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)?
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