[Chimera-users] Color holes in mesh?

Oliver Clarke olibclarke at gmail.com
Fri Apr 8 06:44:10 PDT 2016

I like that, thanks Tom! Doesn't need to be pretty - I mean, it's a bonus,
but not a neccessity - I just want to make sure that for showing density
around a selection I'm not "cheating" - making the density look nicer than
it is by carving too close to the protein - and this is a way of reassuring
the viewer that that is the case.


On Thu, Apr 7, 2016 at 10:39 PM, Tom Goddard <goddard at sonic.net> wrote:

> Hi Oliver,
>   Yes it would be great to be able to highlight the cut edges when showing
> a zone of a density map.  Your technique that uses the
> one-transparent-layer Chimera feature with two transparent surfaces so that
> you only see the colored inside of the surface through the holes is pretty
> tricky.  One thing that is a bit disturbing about that technique is that
> you can only see the cut edges if you are looking into the hole — which is
> slightly mind-bending since you are showing the density as a mesh which one
> sees through.
>   I tried a different idea which is to show the triangles bordering the
> cut edge of the density mesh as a filled green band — image attached.  It’s
> not very pretty, but has the nice attribute that these bands don’t vanish
> depending on the view angle.  The jagged appearance of the bands could
> probably be improved.  I’ve attached the Python script I used to show the
> bands — you make the surface zone, then select the surface, then open the
> script which creates a new surface model representing the bands.  It is not
> very usable but at least lets us test the idea.  Caps that cover the holes
> are tricky because it is hard to define their shape.
>   If we can figure out a pretty and easy technique to show the cut edges,
> I’d love to get it into ChimeraX.
>         Tom
> > On Apr 5, 2016, at 10:04 AM, Oliver Clarke wrote:
> >
> > Hi,
> >
> > 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.
> >
> > Cheers,
> > Oli.
> >
> >
> >
> >
> > <test_carvemap.png>_______________________________________________
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