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

[Kenji MATSUI]

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,）.

[image: image10.png]


[image: 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: 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.rbvi.ucsf.edu/pipermail/chimera-users/attachments/20220720/31a8dde6/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image10.png
Type: image/png
Size: 737922 bytes
Desc: not available
URL: <http://www.rbvi.ucsf.edu/pipermail/chimera-users/attachments/20220720/31a8dde6/attachment-0003.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 93103 bytes
Desc: not available
URL: <http://www.rbvi.ucsf.edu/pipermail/chimera-users/attachments/20220720/31a8dde6/attachment-0004.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 402993 bytes
Desc: not available
URL: <http://www.rbvi.ucsf.edu/pipermail/chimera-users/attachments/20220720/31a8dde6/attachment-0005.png>