[Chimera-users] Chimera bug report submission

[Kenji MATSUI]

Dear Chimera X

I apologize for the very late reply.

Thank you for your kind reply. It is very helpful that you sent me a
screenshot so that I can understand.

Thank you for your continued support.
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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


2021年12月21日(火) 4:07 Elaine Meng <meng at cgl.ucsf.edu>:

> Hi Kenji,
> This is not a bug.  This is because your ligand and receptor molecules are
> not together in a single model, whereas if you use the same structure that
> the tutorial is using (or any of many other complexes from the Protein
> Databank), the ligand and receptor are together in the same model.
>
> If you want to follow the tutorial but with your structure, you would need
> to combine the ligand and receptor into one model.
>
> Actually your session contains 10 models, one receptor (#0.1) and 9
> ligands (#0.2, #0.3 ... #0.9).  I can see this by opening the Model Panel
> and clicking the "group/ungroup" button on the right, and then using the
> "S" checkboxes to show and hide each one so that I can see what they
> contain.  Maybe the ligands are all exactly the same as each other, or at
> least they seem to be quite similar.
>
> Here are some example Chimera commands that would combine #0.1 and #0.2 to
> make a new model #1 and then close all of #0.1-9:
>
> combine #0.1,0.2 ref #0.1 model #1
> close #0
>
> Now you have one new model #1 with both the receptor (that was originally
> #0.1) and the ligand (that was originally #0.2).  If the other ligands are
> different, you would need to repeat the combining process for each one if
> you want to use the same approach to analyze them.
>
> Chimera does not automatically recognize this specific ligand as "ligand"
> (I don't know why), but you can select it by its residue name LIG with
> menu: Select... Residue... LIG, or command:
>
> select :LIG
>
> Also, by default FindHBond will automatically find ALL of the H-bonds.  It
> does not care what is selected unless you turn on the option "Only find
> H-bonds..."  e.g. "with at least one end selected".  You should also turn
> on "If endpoint atom hidden, shown endpoint residue" or else it will not
> show all of the H-bonds it finds.  For this ligand, it finds 2 H-bonds as
> shown in the attached screenshot, with details written to Reply Log.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
> On Dec 20, 2021, at 9:07 AM, Eric Pettersen via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
>
> Begin forwarded message:
>
> From: Kenji Matsui <s214903z at st.go.tuat.ac.jp>
> Subject: Chimera bug report submission
> Date: December 19, 2021 at 11:33:41 PM PST
> To: chimera-bugs at cgl.ucsf.edu
>
> The following bug report has been submitted:
> Platform:        windows_x86_64
> Chimera Version: 1.16
> Description
> I would like to see the interaction between the ligand and the protein,
> but I was not able to display it in the way described in the tutorial. How
> can I do that?
>
> Method
> select →ligand
>
> Tool  Structure analysis Find H-bond Line length 3.0 Å
>
> check  Relax H-bond ~, Only find, Include intera-molecular, Include
> intra-residue
>
> apply →OK
> File attachment: osh4,OSW-1220.py
>
> <osh4,OSW-1220.py>
>
>
>
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