[chimerax-users] How to draw the surface of cavity

[令怡]

Dear Elaine，


Your suggestion about the smoothing surfaces command is very useful, and I could draw the figure exactly what I want. 


I have another question. The map surface is discontinuous because of the low resolution sometimes(see below). If I could creat a close surface? It is improved slightly when I used the smoothing surfaces command. Do you have a better solution? 


Thanks again for your kind detailed reverting！


Best Regards,
Lingyi






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Xu, Lingyi
Ph.D.
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Zhejiang University School of Medicine
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On 4/1/2022 00:58，Elaine Meng<meng at cgl.ucsf.edu> wrote：
Hi Lingyi,
Sorry, ChimeraX does not have an option to make the insides of helix ribbons a different color.

For your other question about smoothing the map output from 3vee: when you use the 3Vee channel finder, there is an option "Grid resolution" where the default is "low".  I believe you will get a smoother result using "medium" and smoothest using "high"

<http://3vee.molmovdb.org/channelFinder.php>

Chimera and ChimeraX do have surface-smoothing options, but they can change the shape a little bit, so it is probably best to first try increasing the resolution of the 3vee calculation, as described above.  Then, if you still wanted to try more smoothing, see the surface and mesh display options of the "volume" command in ChimeraX:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsurf>

The first 5 options in that section relate to smoothing surfaces.

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 31, 2022, at 6:02 AM, 令怡 via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:

Elaine,

Thank you for your instructions and they are very detailed and useful.

I tried them and (2c) has the best effect in my case. But when I display the cavity map in chimera or chimeraX, the surface of cavity is not smooth (see below). I used the smooth tools in the menu bar, but it worked not very well. If it's concerned about "display as isosurface" as your metion, which I know little about that.

There's another question, how to change the helix inside color in cartoon with ChimeraX? I know it can be done with the command "ribinsidecolor" in Chimera.

Thank you for your answer in advance!

Beat Regards,
Lingyi

<299A2A06-DE29-4CA4-8A7F-1DB113B7975C.png>

Xu, Lingyi
Ph.D.
Zhejiang University School of Medicine

On 3/31/2022 00:12，Elaine Meng<meng at cgl.ucsf.edu> wrote：
Hello Lingyi,
ChimeraX and Chimera do not have easy ways to show cavity surfaces, unfortunately.  But there are a few related possibilities:

(1) show molecular surface, but not the whole thing, only for the atoms that surround the cavity.  If the cavity is completely closed by surrounding protein, then it looks pretty nice.  However, in most cases there are openings so you may get uneven edges from surface triangles.  ChimeraX does not have a way to cleanly draw the boundary between the pocket surface and the surrounding surface.

Example with ligand in pocket:
open 2gbp
surface protein & ligand :<4 visiblePatches 1

If you don't have a ligand in the pocket to define a distance zone (4 Angstroms above) you would instead need to list all the residues/atoms of the protein that form the pocket, which can be difficult.

(2) use a separate web server to identify pockets or calculate a blob that fills a cavity, and then open the results.  

(2a) show CASTp-calculated pockets -- this also works by showing partial molecular surfaces in Chimera.  Chimera has a nice tool for looking through the pockets
<http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/castp.html>

Chimera example:  
open castp:2gbp

ChimeraX does not have this feature, but if you did it in Chimera and displayed the pocket(s) that you want, then you could try Chimera export to ChimeraX, Chimera menu: File... Export Scene, choose the ChimeraX option.
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html>

(2b) MOLEonline server does this but it also makes files for Chimera, not ChimeraX (again, maybe you can use the export from Chimera to ChimeraX).
<https://mole.upol.cz/>

(2c) 3Vee server makes a map that fills pockets, which I believe you could open in either Chimera or ChimeraX and then display as isosurface.
<http://3vee.molmovdb.org/>

There are probably other servers that I haven't found.
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 29, 2022, at 10:53 PM, 令怡 via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:

Dear ChimeraX Staff,
Hello! I would like to know if there's a way to display the cavity like this? I've been studying for a long time without a clue.
Thank you for your attention!
Best Regards,
Lingyi
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