[Chimera-users] Video about masking

Tom Goddard goddard at sonic.net
Thu Dec 5 17:59:23 PST 2019

Hi Krishan,

  If you have an tentative atomic model fit into your map you could compute a low resolution simulated map from the atomic model (molmap command) and use the surface of that simulated map to mask the density (mask command).  For example

	open emdbID:20541
	open 6pzz
	molmap :.A-D 10
	mask #0 #1.1

Not sure what type of mask you need.  If you need a volume of ones and zeros the mask command with the "ones" option can make that.

	https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/mask.html <https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/mask.html>

	https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>

  Not sure what you mean volume eraser does not delete anything.  Position the sphere with mouse and press the Erase button to erase -- it makes a new copy of the map with part erased that you could save to a file.  But I wouldn't recommend that approach if you have an atomic model.


> On Dec 5, 2019, at 11:33 AM, Krishan Pandey <krishan.pandey at health.slu.edu> wrote:
> Hi
> I am kind of new to Chimera and was wondering if there is a video tutorial about creating a mask in Chimera. I intend to use the mask for local resolution or multi body refinement. To experienced users this may be a novice question. I tried to search online but could find any. When I use volume eraser to delete part of EM map, it does not do anything, nothing is deleted.
> I am using Chimera 1.13.1 (build 41965).
> Any help is appreciated.
> Thank you
> Krishan Pandey
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