[Chimera-users] Display channel as a filled body in Chimera

Elaine Meng meng at cgl.ucsf.edu
Fri Mar 23 09:20:31 PDT 2018

Hi Boaz,
The CastP tool just takes the atoms listed as lining the pocket and then shows their molecular surface patches, so what you get may not be a closed surface unless the molecular surface of those atoms really does form an enclosed bubble.

For approaches to get an enclosed surface even when the molecular surface does not form an enclosed bubble, please see the last part of this previous post:

It mentions (A) Surfnet tool in Chimera (B) VVV website to calculate a map filling the space.

Unfortunately showing a cavity blob in Chimera is not as convenient as using HOLE, HOLLOW, CAVER etc. with Pymol since those tools have Pymol plugins.  In this previous post, Oliver Clarke provided a script for visualizing HOLE results in Chimera:
… see also <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-August/011375.html>

Yet another possibility outside of Chimera is MolAxis.  At least when I used it a long time ago, it took only minor editing to display in Chimera, as described for this entry in the Image Gallery:

MolAxis server: <http://bioinfo3d.cs.tau.ac.il/MolAxis/>

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 23, 2018, at 6:57 AM, Boaz Shaanan <bshaanan at bgu.ac.il> wrote:
> Hi, 
> Is there a way to display in Chimera a channel identified by CastP as a filled body rather than engulfed by a surface?
> Thanks,
>              Boaz

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