[Chimera-users] Question: How ro show the H-bond

[Kenji MATSUI]

Dear Chimera company

Thank you for always answering my questions so carefully.
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 entered the data as per the manual. However, the hydrogen bond did not
show up. What should I do?

The figure of Parameters

[image: image.png]

The result of showing
[image: osh4,ID 223-230 .png]

Details on how to do it

*Display interactions between ligand and protein.*

1.Favorites→Model Panel→group/ungroup( Go down at close.)
[image: image.png]

2.Favorite→Command line: combine #0.1,0.2

→select combination at model Panel
[image: image.png]



3.rename

4.Select →Residue→ LIG or command: select :LIG

5.Tool→Surface/Binding Analysis→ Find H Bond
[image: image.png]

Check three points

1."Only find H-bonds..."  e.g. "with at least one end selected".

2.  "If endpoint atom hidden, shown endpoint residue" or else it will not
show all of the H-bonds it finds

3.Write information to reply log

Apply→OK

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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
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