[Chimera-users] Question: Why hydrogen bonds are not displayed?

[Kenji MATSUI]

Dear Chimera

Thank you for taking the time to contact us.

I'm Matsui.

I changed the value of RELAX and it is now displayed.

Thank you for taking your time.

---------------------------------------------------------------------------
Kenji Matsui
Graduate School of Tokyo University of Agriculture and Technology M2
2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
 Mail: s214903z at st.go.tuat.ac.jp


2022年10月17日(月) 1:49 Elaine Meng <meng at cgl.ucsf.edu>:

> Hi Kenji,
> There is no single agreed method for finding H-bonds.  Different people
> may use different methods and parameter values, so it is not surprising if
> your calculations give different results sometimes.  However, we allow
> people to adjust parameters with the "Relax H-bond constraints" section.
> You just need to experiment with increasing the values if you want to find
> a specific result.
>
> In this case, you can find this "H-bond" by increasing the relax values to
> 1.5 angstroms and 45 degrees.  It has both a long distance and a poor angle.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> > On Oct 15, 2022, at 2:54 AM, Kenji MATSUI via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > Dear Chimera
> >
> > I am sorry to interrupt your busy schedule.
> >
> > My name is Matsui, and I am a second-year master's student at a Japanese
> university.
> > Thank you for taking time out of your busy schedule to respond to my
> question the other day.
> >
> > I am now looking at protein-ligand interactions.
> >
> > We found in the paper that His 421 interacted with another ligand.
> >
> > Therefore, the interaction between His-421 and the ligand.
> >
> > Problem :However, no hydrogen bonds were displayed.(first figure)
> >
> > I would like you to ask why this is caused.
> >
> > ----------------------------------------------------------
> > <detail>
> > This is because the distance between the His-421 and OH oxygen atoms was
> 3.7 Å.
> > A ligand with a structure similar to this one in the paper formed a
> hydrogen bond with His-421 at 3.8 Å.
> >
> > The thing  I tried
> > The Relax H-bond constraints section was adjusted from 3.0 to 5.0.
> >
> >
> > <image.png>
> > you can show this figure when you open the attached file
> >
> > Wheat: Ligand  the other color:protein
> >
> > <image.png>
> >
> > H-bond parameter
> > <image.png>
> >
> >
> ---------------------------------------------------------------------------
> >
> > Kenji Matsui
> >  Graduate School of Tokyo University of Agriculture and Technology M2
> > 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
> >  Mail: s214903z at st.go.tuat.ac.jp
> >
> <LXRα_25-HC(overlay_1P8D).py>_______________________________________________
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>
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