[Chimera-users] chimera

Tom Goddard goddard at cgl.ucsf.edu
Wed Apr 2 11:09:58 PDT 2008

Hi Somnath,

  You need to set the correct grid plane spacing for your EM map to make 
its size match the crystal model.  Use the Coordinates panel of the 
volume dialog and set the "voxel size" to the distance between adjacent 
grid planes in Angstroms.  Probably the current setting is 1 Angstrom -- 
the default when no value is specified in the map file header.  The 
people who determined the EM map will know the correct value, probably 
roughly 8 Angstroms for a map with 22 Angstrom resolution.  After typing 
in a new voxel size value press the Enter key to see the map scaled to 
the new size.

  The contour level does not control the size of the map.  It sets the 
data value at which the surface is shown.  Lower values will make a 
larger surface because you are including more low signal level data at 
the periphery of your structure.   You can use any contour level.  
Sometimes you might choose it to enclose a specific volume based on the 
molecular weight of the imaged object (use Tools / Volume Data / Measure 
Volume and Area) or you might set it to 1.0 standard deviation above the 
mean value (use Tools / Volume Data / Volume Mean, SD, RMS).


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