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

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 27 14:22:04 PDT 2018

Hi Boaz,
Glad you made some headway.

surfcat command specifies groups of atoms to enclose in a surface, e.g. myglobin could be enclosed without the heme, or myoglobin + heme could be enclosed in one “blob” together.  It does not specify which atoms’ surface is shown, only how they are grouped for surface-calculation purposes.  Surfcat categories are mutually exclusive (an atom only belongs to one category), and most people just use the ones calculated automatically, without using the surfcat command explicitly.

surface command specifies which atoms’ surface patches are shown, after the surface is calculated enclosing the set of atoms in a surface category

Both commands can take “sel” as an atomspec, meaning the currently selected atoms.

I haven’t tried this with HOLE plus Oliver’s script, so can’t be absolutely certain how it would turn out, but “in theory” it sounds reasonable.  E.g. I have no idea what radii the dots are assigned, you may have to fiddle with that using the vdwdef command.s

Another possibility is to just use “molmap” command (simulate density for those atoms, show isosurface that can be adjusted in Volume Viewer).
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 27, 2018, at 1:45 PM, Boaz Shaanan <bshaanan at bgu.ac.il> wrote:
> 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?
> Thanks,
>             Boaz
> ________________________________________
> 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:
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-May/010993.html>
> 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:
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-August/011373.html>
> … 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:
> <http://www.rbvi.ucsf.edu/chimera/ImageGallery/entries/cavities/cavities.html>
> MolAxis server: <http://bioinfo3d.cs.tau.ac.il/MolAxis/>
> I hope this helps,
> Elaine
> -----
> 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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