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

[Elaine Meng]

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>_______________________________________________
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> 
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