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

Boaz Shaanan bshaanan at bgu.ac.il
Tue Mar 27 13:45:16 PDT 2018

Hi Elaine,

Your advice about displaying a channel as a filled body was very useful. Using HOLE and Oliver's script I managed to get a satisfactory display of a channel. Now I'd like to do two things using surfcat (if I got right the purpose of this command):
1) The channel display I have is a bunch of little balls that can be treated as atoms. I can select them but can I tell surfcat about this selection? How? I hope to then be able to cover them by a surface or is that too much to ask?

2) I select protein atoms in contact with the channel (using zone) which I'd like to display as a surface. Again, how can I tell surfcat about the selection?

Or have I totally misunderstood the surfcat command action?



Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105

E-mail: bshaanan at bgu.ac.il
Phone: 972-8-647-2220
Fax:   972-8-647-2992 or 972-8-646-1710

From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Friday, March 23, 2018 7:20 PM
To: בעז שאנן
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Display channel as a filled body in Chimera

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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