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

[Kenji MATSUI]

Dear Elaine

Thank you for taking the time to reply.

Based on the method you taught me, I have displayed it as shown in the
figure below.

*Command*: *~ribbon
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ribbon.html>*

[image: image3.png]

I am very sorry,

I'm thinking of cropping out half of this surface because I want to show
the surface clearly, but what should I do to have the diagram output as
described in the paper for the second photo?


[image: image.png]

What I did.

I went through the tutorial on Chimera.
I tried to display it in clip, but it did not work
---------------------------------------------------------------------------
松井 健治
 東京農工大学大学院 工学府産業技術専攻 修士 2年
〒184-8588 東京都小金井市中町2-24-16
 Mail: s214903z at st.go.tuat.ac.jp


2022年7月20日(水) 23:59 Elaine Meng <meng at cgl.ucsf.edu>:

> 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
>
>
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