[Chimera-users] superimposing protein structures

Elaine Meng meng at cgl.ucsf.edu
Wed Jan 5 18:09:57 PST 2022

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:

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, 

...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:

There are some tutorials that use MatchMaker, for example

I hope this helps,
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>_______________________________________________
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