[Chimera-users] Map Orientation for Symmetry Plug-in

Thomas Goddard goddard at cgl.ucsf.edu
Mon Feb 5 19:54:33 PST 2007

Hi Albion,

   Chimera doesn't currently have a method for locating the symmetry 
axis of a map.  But I have an idea of how to do it that is very simple. 
  There is in Chimera version 1.2318 a new tool to fit one density map 
in another.  If you open your map with symmetry, then open a second copy 
of the map (the volume dialog File / Duplicate is an easy way to do 
that), then rotate and shift the second copy by approximately one 
periodic unit by hand, then use the "fit map in map" tool to optimize 
the fit, you get the transformation matrix that generates the symmetry. 
  The "fit map in map" tool prints that transformation matrix to the 
Chimera Reply Log (Favorites / Reply log) as a 3 by 4 matrix.  But I 
could easily also have it print the transformation as a rotation axis 
vector, a point on the rotation axis, an angle of rotation, and a shift 
distance along the axis.  The axis point would lie on the symmetry axis. 
  You could then shift the origin of the map so this point was at 
(0,0,0) using the volume dialog Features / Origin and Scale.  And you 
could save it as a new MRC map if you wanted that origin in the header.

   Usually the map was created with symmetry imposed in the 
reconstruction and it is of course better to simply know the exact 
symmetry axis that was used to create the map.  But the above technique 
will help when that information is hard to figure out.

   I already have code that determines the axis, angle and shift so it 
should be easy to have that printed out by the "fit map in map" tool. 
I'll look into it tomorrow and perhaps be able to send you some new 
Python code if you would like to try it.


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