Hi Xiangan, The mask command is working fine in my tests. It only sets the map values to zero outside the surface. The values inside the surface are identical to the original map. If that is not the case for you than use menu Help / Report a Bug... and provide the exact mask command you used and explain how you know that the new masked map values are different from the original map. This sounds like the right approach to segmenting a subunit. If instead you had a fit atomic model you could use Color Zone and the Split button on that dialog. Tom

Hi Tom, I am trying to use your MASK command to extract some interested volumes from a density map based on another reference density map.

http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/mask.html

I followed your guide line from the link above, but the extracted density is not the same as the original density. Is there anything I should pay special attention? It looks like the command was created many years ago, is it still good for the latest chimera version?

Do I have any other way to segment map based on a known subunit density map, something similar to color zone?

Thanks,

Xiangan Liu