[Chimera-users] volume viewer question

Tom Goddard goddard at sonic.net
Tue Aug 24 17:53:32 PDT 2010

Hi William,

   The volume data values Chimera shows in the volume dialog histogram 
are just the values found in the map file.  They are not in sigma 
units.  You can measure the root-mean-square value for a unit cell map 
with menu entry Tools / Volume Data / Measure Mean, SD, RMS and divide 
the reported values by the RMS to get sigma units.  This is a pain.  The 
reason it doesn't work better is because Chimera map display was 
primarily developed for electron microscopy where sigma values are not 
easily defined as in crystallography.


> Hello,
>   I am trying to make an electron density figure using chimera and 
> need to contour the F0-Fc map to 3 sigma.  How can you determine the 
> sigma level displayed with the volume viewer? The levels appear to be 
> different than that observed when using coot or Xtalview.
> Thank you,
> William Snee

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