[Chimera-users] mask command

Tom Goddard goddard at sonic.net
Thu Dec 13 16:15:56 PST 2012

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.


> 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

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