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

[Boaz Shaanan]

Hi Elaine,

As usual, wonderful suggestions. I'll try them. As for the radii of these balls in the channel from HOLE, I can change those after selecting them using the little green square on bottom right.

Again, thanks a lot for your help.

            Boaz



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

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: Wednesday, March 28, 2018 12:22 AM
To: בעז שאנן
Cc: chimera-users at cgl.ucsf.edu Mailing List
Subject: Re: [Chimera-users] Display channel as a filled body in Chimera

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.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/msms.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/surface.html#surfcats>

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
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html>

Another possibility is to just use “molmap” command (simulate density for those atoms, show isosurface that can be adjusted in Volume Viewer).
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
Best
Elaine
-----
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