[Chimera-users] Color holes in mesh?

Oliver Clarke olibclarke at gmail.com
Tue Apr 5 10:04:37 PDT 2016


When I want to show electron density around, for example, a single alpha
helix in a structure, there are a couple of options in chimera - one would
be to use vop zone, which I don't like for this purpose, because it creates
a new map that can be recontoured (so one can't see where the original map
has been cut). The sop analog of this, sop zone, works quite well for the
purpose, but there is no easy way that I can find to cap the holes that are
created in the mesh - I want to do this so that I can make it obvious where
"carving" the map has affected the shape of the resultant map, or has
truncated connected regions that are not displayed.

Would it be possible to add such an option in ChimeraX? Or having an option
to represent the inside of a surface differently from the outside would do
the trick also.

For the moment I have a work around (used in the attached pic):
1. Create a mesh.
2. Duplicate the mesh, change to surface rep and set transparency to 0.001.
3. Create a copy of this surface, change the transparency to 0.99 and
increase the volume level by 0.001.

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