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

[Elaine Meng]

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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