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
Hi William, The values in the Volume Viewer histogram are not normalized by sigma; they are just the raw values in the density map file. However, Chimera can report the mean and standard deviation, and then you can use those values to manually calculate what level corresponds to a given sigma. Please see these previous posts for more details: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2008-May/002651.html> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-February/004765.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Aug 24, 2010, at 12:29 PM, William Snee wrote:
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
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. Tom
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
participants (3)
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Elaine Meng -
Tom Goddard -
William Snee