[Chimera-users] superimposing protein structures
Kenji MATSUI
s214903z at st.go.tuat.ac.jp
Wed Jan 5 19:43:17 PST 2022
Dear Elaine C. Meng, Ph.D.
Thank you for your quick response. I'll try it with Matchmaker.
Thank you for your kind attention.
---------------------------------------------------------------------------
松井 健治
東京農工大学大学院 工学府産業技術専攻 修士
〒184-8588 東京都小金井市中町2-24-16
Mail: s214903z at st.go.tuat.ac.jp
Kenji Matsui
Graduate School of Tokyo University of Agriculture and Technology
2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
Mail: s214903z at st.go.tuat.ac.jp
2022年1月6日(木) 11:10 Elaine Meng <meng at cgl.ucsf.edu>:
> Hi Kenji,
> That Match->Align tool makes a sequence alignment. That is not what you
> want. You want to put structures on top of each other, and probably the
> easiest way to do it is with the MatchMaker tool (menu: Tools... Structure
> Comparison... MatchMaker).
>
> Here is the general discussion of different methods in Chimera to put
> structures on top of each other:
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
>
> Next after showing the Matchmaker tool, you need to decide which one stays
> in the same place and which one gets moved on top of it. I don't know if
> the docked ligand (light blue) and gray protein are together in one model
> or in two separate models. Since the PDB complex (pink) is one model it is
> probably simplest to tell the tool to move the pink one.
>
> In the Matchmaker dialog,
> <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html
> >
>
> ...choose the gray protein as Reference model and choose the pink one as
> Structure to Match (I can't tell which model numbers they have, you will
> have to look in the Model Panel to figure it out, menu: Favorites... Model
> Panel). Then click OK to just use default options. They will probably
> give what you want. If not, you can try again later with different options.
>
> There is also a "matchmaker" command that does the same thing as the tool:
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html>
>
> There are some tutorials that use MatchMaker, for example
> <
> https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/alignments.html
> >
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
>
> > On Jan 5, 2022, at 5:39 PM, Kenji MATSUI via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > Dear Chimera company
> >
> > Thank you for allowing me to use your software. I am Japanese, so I hope
> you will understand that there are some inappropriate expressions. I would
> like to ask you one question.
> >
> > I would like to know how to overlay the docked protein (osh4)-ligand
> (cholesterol) complex (the gray one in the figure) and the complex on the
> PDB.
> >
> >
> > <image.png>
> >
> > Aim
> > I would like to know how well the docked data matches the data in the
> PDB.
> >
> > Methods I have tried
> >
> > I did it based on the following link from Chimera.
> >
> >
> https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchalign.html
> > Thank you for your cooperation.
> >
> ---------------------------------------------------------------------------
> > 松井 健治
> > 東京農工大学大学院 工学府産業技術専攻 修士
> > 〒184-8588 東京都小金井市中町2-24-16
> > Mail: s214903z at st.go.tuat.ac.jp
> >
> > Kenji Matsui
> > Graduate School of Tokyo University of Agriculture and Technology
> > 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
> > Mail: s214903z at st.go.tuat.ac.jp
> > <osh4_cholesterol.chimerax><Osh4 with
> cholesterol.pdb>_______________________________________________
> > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> > Manage subscription:
> https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
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