[chimerax-users] [Chimera-users] How to caluculate buried surface area

[Kenji MATSUI]

Dear Elaine

Thank you for replying.

I'm Matsui.

I apologize for my misunderstanding.

I understand.
---------------------------------------------------------------------------
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8日(木) 0:58 Elaine Meng <meng at cgl.ucsf.edu>:

> Dear Kenji,
> The example commands in my previous message are for ChimeraX, not Chimera.
> Elaine
>
> > On Sep 7, 2022, at 7:06 AM, Kenji MATSUI via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > 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
> >
> > _______________________________________________
> > 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/chimerax-users/attachments/20220908/ae1dada2/attachment.html>