You can choose a map contour so it encloses the expected number of cubic Angstroms as described here:

http://www.cgl.ucsf.edu/chimera/data/tutorials/eman07/chimera-eman-2007.html#part2

Tom

Hello,

My name is Rakesh. I would like to know how to set the density threshold according to the molecular mass of the protein in the cryoem map. I would also like to know how to calculate the molecular mass of a particular segment after segmentation in cryoem map.
Regards
Rakesh Ramachandran
PhD Student
Molecular Biophysics Unit,
Indian Institute of Science,
Bangalore - 560012
India