[Chimera-users] How to caluculate buried surface area

[Kenji MATSUI]

Dear Elane

Thank you for your time and response.

My name is Matsui, and I am a second-year master's student at a Japanese
university.

 I am also using ChimeraX.

 But first I will try the method you showed me with chimera, and if it
doesn't work, I will try it with chimeraX as well.
---------------------------------------------------------------------------
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


2022年9月6日(火) 23:30 Elaine Meng <meng at cgl.ucsf.edu>:

> 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
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.rbvi.ucsf.edu/pipermail/chimera-users/attachments/20220907/5fd4c207/attachment.html>