[Chimera-users] How to show ligand pocket as wireframe mesh

[Elaine Meng]

Hi Leif,
I’m guessing you just want to show the molecular surface of the pocket.  Although there is a tutorial that includes showing the surface of a ligand pocket (see “surfaces and attributes” section):

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>

… the tricky part is how to show only part of the surface instead of the surface around the entire receptor, for which the process would be slightly different from case to case. The tutorial also shows a solid surface, but you can just make it transparent or mesh using choices within the "Actions… Surface” menu.  "Actions.. Surface… show" will show you the surface in the first place, either the whole surface if you don’t have any atoms selected, or if you do have atoms selected, for just those atoms.

If the entire surface was already shown, you could probably use a similar “sop zone” command as shown in that tutorial to limit it to the are near your docked ligands, except instead of  the word “ligand” you’d give the model number of your docked ligands.

You might also take a look at one or more of the Getting Started tutorials which cover things like showing and hiding different representations.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html>
- or -
<http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html>

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

> On Sep 19, 2018, at 9:13 AM, leifepeterson at sbcglobal.net wrote:
> 
> I ran a ligand-receptor prediction for a protein at Site-hound, and downloaded all the files.   Is there a Chimera tutorial which shows how to display the volume a selected cluster inside the protein as a wireframe mesh?   My guess is that the volume will be between all the AA residues in the given cluster(?)   
>  
> Once I can show the mesh, I will then go through the Autodock Vina run using ligands in a mol2 file, to sort their energies.