Hi Dmitry, Depends what you mean by “compare.” Some thoughts are: (A) subtract one map from the other to see the differences: command “vop subtract” <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#subtract> (B) show the same isosurface level for both, Measure Volume and Area (under Tools… Volume Data) or the corresponding commands “measure volume” “measure area” <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/measurevol/measurevol.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#volume> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#area> (C) morph between their isosurfaces with Morph Map tool or command “vop morph" <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morphmap/morphmap.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#morph> This tutorial has an example of morphing between two EM maps (about halfway down the page): <http://www.rbvi.ucsf.edu/chimera/data/tutorials/eman07/chimera-eman-2007.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Feb 28, 2020, at 1:58 AM, Dmitry Semchonok <Semchonok@gmail.com> wrote:

Dear colleagues, I have similar cryo-em maps that have also some differences. I want to compare them. Is there a tool in chimera that can compare the cryo-em maps? Thank you! Sincerely, Dmitry