[Chimera-users] How to examine the hydrophobicity and hydrophilicity around the ligand

[Elaine Meng]

Hi Kenji,
There is no need to apologize for the time of the message -- no matter when you send it, I can wait to answer until I am at work.

Yes, that is a common problem with showing parts of the surface.  There is no simple solution, you just have to try showing and hiding different parts of the surface. Sometimes you can rotate the structure so that the clipping (where the front is sliced off) is at a better position to show the pocket.  Even if you turn off clipping, sometimes it is possible to hide the outer surface and show only the pocket, but it depends on the shape of the surface.  

There is an example in the Structure Analysis and Comparison tutorial, in the "Surfaces and Attributes" section, of showing only the pocket surface around the ligand:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html#surfaces>

That example uses "sop zone" to show only the surface of receptor atoms within 5 angstroms of ligand; you could use some other distance if it looks better in your structure..  Again, however, whether that looks good enough depends on the shape of the surface and the pocket.

If you want to turn off  the front/back clipping, you can use command "clip off".   Another thing you can try (but that would also take time to experiment) is Per-Model Clipping tool, where you can turn on a clipping plane, but then rotate it by hand to any angle.  You can make the clipping plane only affect the surface and not the atoms.
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/per-model/per-model.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 Jul 20, 2022, at 12:17 AM, Kenji MATSUI via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear Chimera
> 
> Thank you for taking the time to answer my question the other day.
> 
> I also apologize for contacting you outside of business hours due to the time difference.
> 
> I'm Kenji Matsui, a second-year master's student at a national university in Japan.
> 
> I am looking at ligand-protein interactions and how they affect binding affinity.
> 
> Therefore, I would like to examine the hydrophobicity and hydrophilicity around the ligand in the figure below（second photo,）.
> 
> <image10.png>       
> 
> 
> <image.png>
> 　　　　second photo
> 
> 
> Methods Tried
> select→ligand→Focus
> 
> This method causes some parts of the surface to be difficult to see.
> As shown in the second photo, it is difficult to see the degree of hydrophobicity around the ligand.
> 
> <image.png>
> 
> Please confirm.
> 
> ---------------------------------------------------------------------------
> Kenji Matsui
>  Graduate School of Tokyo University of Agriculture and Technology　M2
> 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
>  Mail: s214903z at st.go.tuat.ac.jp