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

[Kenji MATSUI]

Dear Elaine C. Meng, Ph.D.

Thank you for your kind reply.

I was able to do it by trying it myself.

Thank you for your continued support.
---------------------------------------------------------------------------
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15日(土) 2:08 Elaine Meng <meng at cgl.ucsf.edu>:

> Hi Kenji,
> The structure you sent  <ID1, 122.pdb>  works fine for me.
>
> The ligand and receptor are already together  in one model and there is
> one H-bond with default "relax" values, see screenshot:
>
>
> 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 14, 2022, at 1:02 AM, Kenji MATSUI via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
>
> Dear Elaine C. Meng, Ph.D.
>
> I am very sorry for the delay in replying, as I have not been notified.
> I would like to thank you again for your kindness and support.
>
> I can't tell what is happening with the structure in the first (top)
> ribbon/stick image that you sent without having the data (e.g. a session).
> >My apologies for not attaching the data. I will attach the data. However,
> I will try to do what you explained first by myself, so you don't need to
> analyze it. Thank you for taking the time to respond.
>
> In the bottom three images you sent, with the details of what you did, the
> last image shows H-bonds in the graphics window and in the Reply Log.  So
> there is no problem for those, right?   The only strange thing is that in
> the Model Panel image there are four lines for "combination" model #1 when
> I would expect only one.  You should probably close the original models and
> the extra combination models so that you only have one "combination" model
> when you do the H-bonds calculation.
> ＞Thank you for your kind explanation. I will try it.
>
> For the structure in the first (top) image, the only ideas I have are
> (1) maybe you did not make it into a combination model.  I.e. if the
> ligand is 0.1 and the receptor is 0.2, it will not find the H-bonds between
> them.
> (2) maybe there really aren't any H-bonds.  You could try increasing the
> "Relax" values if you think there are H-bonds but the distances are
> slightly too long or the angles are not optimal for H-bonding
>
> ＞I hadn't thought about the cause of (1), so I'll look into it.
> As for (2), since I'm a beginner, I've only tried to set Relax to 3.0 in
> the manual, so I'll try this too.
>
> ---------------------------------------------------------------------------
>
> 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12日(水) 1:47 Elaine Meng <meng at cgl.ucsf.edu>:
> Hi Kenji,
> I am confused by your question.
>
> I can't tell what is happening with the structure in the first (top)
> ribbon/stick image that you sent without having the data (e.g. a session).
>
> In the bottom three images you sent, with the details of what you did, the
> last image shows H-bonds in the graphics window and in the Reply Log.  So
> there is no problem for those, right?   The only strange thing is that in
> the Model Panel image there are four lines for "combination" model #1 when
> I would expect only one.  You should probably close the original models
> and the extra combination models so that you only have one "combination"
> model when you do the H-bonds calculation.
>
> For the structure in the first (top) image, the only ideas I have are
> (1) maybe you did not make it into a combination model.  I.e. if the
> ligand is 0.1 and the receptor is 0.2, it will not find the H-bonds between
> them.
> (2) maybe there really aren't any H-bonds.  You could try increasing the
> "Relax" values if you think there are H-bonds but the distances are
> slightly too long or the angles are not optimal for H-bonding.
>
> 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 10, 2022, at 6:33 PM, Kenji MATSUI via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > 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.png>
> >
> > The result of showing
> > <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.png>
> > 2.Favorite→Command line: combine #0.1,0.2
> > →select combination at model Panel
> > <image.png>
> >
> > 3.rename
> > 4.Select →Residue→ LIG or command: select :LIG
> > 5.Tool→Surface/Binding Analysis→ Find H Bond
> > <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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