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. Cheers, Oli On Thu, Apr 7, 2016 at 10:39 PM, Tom Goddard <goddard@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.
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