[Chimera-users] How to caluculate buried surface area

[Kenji MATSUI]

Dear Chimera

I am sorry to interrupt your busy schedule.

My name is Matsui, and I am a second-year master's student at a Japanese
university.
Thank you for taking time out of your busy schedule to respond to my
question the other day.

We are investigating the buried surface area to see the magnitude of the
interaction between protein and ligand.

For this purpose, I calculated the solvent accessible area of the ligand.
However, the value is 9955, which shows the entire surface area of the
protein.

What should I do? I am not in a hurry for answers , so I would appreciate a
reply when you have the time.

In this case, the ligand was in the binding pocket of the protein, so I
would like to calculate the ligand's solvent contact area = buried surface
area.

I tried to check and tried , but it did not work.

1.See
https://www.cgl.ucsf.edu/pipermail/chimera-users/2009-January/003521.html

2.Try to use measure blob  using chimera X.
Reference:
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea

However, I didn't know how to solve this command.
Command ;ui mousemode right "pick blobs

Reference; https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html
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Kenji Matsui
 Graduate School of Tokyo University of Agriculture and Technology M2
2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
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