[Chimera-users] precalculated void representation as surface

Elaine Meng meng at cgl.ucsf.edu
Tue Aug 2 15:10:39 PDT 2016


On Aug 2, 2016, at 3:07 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Karolina,
> If I understand correctly, you just want to show the “skin” of the pocket but then also what is on the inside.   In that case, do you really need the void-volume atoms?  Why not just show the surface of the protein and slice that surface with the clipping plane? See first attached image.
> 
> However, if the protein is completely hidden and you just want the skin of the pocket, a second idea is to keep all the void-volume atoms for calculating the isosurface, but then also hide those fake atoms.   When you slice the molmap isosurface, by default it looks solid because there is a “cap”.  With Surface Capping (in menu under Tools… Depiction) you can just turn off the cap so that you just see the sliced skin of the pocket, and real atoms inside (if any).  See second attached image.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/per-model/per-model.html>

oops, the link above was supposed to be:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfcapper/surfcapper.html>

> 
> In both cases, if you use a per-model clipping plane instead of the main (global) clipping planes, you can slice at any angle and only the surface, so atoms can stick out beyond the clipping plane.  Per-Model Clipping is in the menu under Tools… Depiction.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/per-model/per-model.html>
> 
> I hope this helps,
> Elaine




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