[Chimera-users] coordinates

Tom Goddard goddard at cgl.ucsf.edu
Fri Jan 25 13:59:48 PST 2008

Hi Hernando,

  You have it almost exactly right except one detail.  The origin of 
your map as shown in the volume dialog Coordinates panel should be -300 
-300 0.  This says to place the corner of the map (grid index 0,0,0) at 
xyz position (-300,-300,0) which in turn makes the center of the map 
(grid index 75,75,75) at (0,0,300) since the grid plane spacing is 4.  
Fit your one copy into the map with this map origin, save PDB relative 
to map, edit helical symmetries into PDB file (rotating about z axis 
through 0,0,0), reload that PDB, and use the sym command and it will work.

  In the future Chimera will have a tool so you can specify helical 
symmetry (pitch and axis) and avoid the file editing step.


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