[Chimera-users] mask using volume contour surface

Tom Goddard goddard at sonic.net
Mon May 13 10:25:05 PDT 2013

Hi Gongpu,

  The easiest way to do this is use the "fillOverlap true" option to the Chimera mask command.


"fillOverlap true | false 
When multiple surface pieces are specified, retain the union of the values from masking to each piece separately. For example, if two surface pieces are concentric spheres, fillOverlap true will return values for all grid points within the larger sphere, whereas fillOverlap false will return values for only those points in the shell between the two surfaces."

This sounds like exactly what you want but there is a catch.  Your two layers of the contour surface are not separate Chimera "surface pieces" because a contour surface produces just one "piece".  To split the surface into connected separate pieces you can select the surface (ctrl-click) and use the keyboard shortcut "Sc" (stands for split connected).  You can run that keyboard shortcut without enabling Chimera keyboard shortcuts using the equivalent command "ac Sc".  In the Chimera 1.8 release candidate or Chimera daily build you can use the less cryptic command "sop split #3" (if your surface is model #3).  If your inner and outer shells are actually connected by some tube that runs between them then a trickier procedure would be needed.

Once you've done this splitting into connected pieces business you actually don't need the fillOverlap option to the mask command.  Instead you just select the outer surface piece (ctrl click it) and use "mask #1 sel".  In this command "sel" stands for whatever is currently selected.


On May 11, 2013, at 8:45 PM, gongpu zhao <goz1 at pitt.edu> wrote:

> Hi All,
> I  have a question about volume contour surface in chimera. I have a density volume of a shell shape. I plan to use the outer contour surface of the volume to mask out all density encased by the outer surface in a tomogram. But instead, I could only mask out the density within the shell. I am wondering if I can make a surface model only using the outer surface.
> Thanks a lot.
> Gongpu
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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