[Chimera-users] How to caluculate buried surface area

[Elaine Meng]

Hi Kenji,
You are using ChimeraX?  I CC'd the ChimeraX address chimerax-users at cgl.ucsf.edu (different than chimera-users at cgl.ucsf.edu).

The "measure buriedArea" command does not require picking any blobs.  You just specify the parts that you want in the command line.
<https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea>

So, maybe something like command:

measure buriedarea protein with ligand

...but maybe "ligand" doesn't get your ligand.  You would have to use whatever kind of specification works for your ligand, e.g. if residue name is UNK, something like this instead:

measure buriedarea protein with :UNK

You sent a Pymol session... I don't use Pymol so I can't open that file, sorry.
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 5, 2022, at 9:45 PM, Kenji MATSUI via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> 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
> ---------------------------------------------------------------------------
> Kenji Matsui
>  Graduate School of Tokyo University of Agriculture and Technology　M2
> 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
> 
> <Buried_surface_area_LXRα_1UHL_24,25-epoxy_cholesterol (remove LXRβ_1P8D).pse>_______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users