Hi Dmitry, There are related tools but they all require your input/judgement, rather than identifying the detergent shell automatically. If you already have atoms fitted into the remainder, a few possible different ways: - use Color Zone (split map button) to get a new map retaining only the parts close to the atoms <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html> - show surface for atoms, e.g. molecular surface (or surface of map derived from atoms with "molmap") and then "mask" the original map by that surface <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html> - semiautomated segmentation approaches to segment out only the part(s) you want <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/segger/segment.html> If you don't have atoms fitted: - Volume Eraser for you to do it "manually" <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/voleraser.html> There are also several kinds of map filtering that may also be relevant, see Volume Filter (or "vop" commands): <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/gaussian.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 Jul 16, 2020, at 1:30 AM, Dmitry A. Semchonok <semchonok@gmail.com> wrote:
Dear colleagues,
Is there a way to subtract the detergent shell from the cryo-em map in chimera?
Thank you
Sincerely, Dmitry