[chimerax-users] The problem of ligands disappearing when the file is converted

[Kenji MATSUI]

Dear Elaine

Thank you for your quick reply.

However, my only guess is that in ChimeraX, you did not correctly combine
the receptor and ligand models into one model before saving it as a PDB
file, or that when you saved you didn't save the combined model but some
other model.
>Thank you for telling me exactly what the problem is.

In ChimeraX you have to use the "combine" command to make a new model, and
then save the new model.  There is no GUI for combining yet.  After
combining, then you can use either the "save" command or menu: File... Save
to save the new model.
>Thank you for showing me exactly how to do it. I will do it as soon as
possible.

Thanks to your help, I will be able to make progress in my research.

 Thank you from the bottom of my heart.
---------------------------------------------------------------------------
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) 3:24 Elaine Meng <meng at cgl.ucsf.edu>:

> In ChimeraX you have to use the "combine" command to make a new model, and
> then save the new model.  There is no GUI for combining yet.  After
> combining, then you can use either the "save" command or menu: File... Save
> to save the new model.
>
> My example used commands for both steps:
> <
> https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-December/003032.html
> >
>
> Elaine
>
>
> > On Dec 20, 2021, at 9:46 AM, Elaine Meng via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
> >
> > Hi Kenji,
> > I don't really know how to use Pymol very well, so I can't help with
> that program.
> >
> > However, my only guess is that in ChimeraX, you did not correctly
> combine the receptor and ligand models into one model before saving it as a
> PDB file, or that when you saved you didn't save the combined model but
> some other model.
> >
> > I happened to have an extremely old version of Pymol on my old computer
> (it does not run on my current computer), and when I opened result10.pdb
> saved from your session with exactly the commands I sent you earlier, I
> could see that the ligand was displayed, see screenshot:
> >
> > <Screen Shot 2021-12-20 at 9.32.17 AM.png>
> >
> > The reply I sent before with the exact commands that I used to make the
> file is here:
> > <
> https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-December/003032.html
> >
> >
> > ...and I also attach that file, result10.pdb:  <result10.pdb>
> >
> > 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 19, 2021, at 10:14 PM, Kenji MATSUI via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
> >>
> >> Dear  ChimeraX
> >>
> >> Thank you very much for your kind words in the past. When I opened the
> PDB file and mol2 file saved by pymol using the method you gave me, the
> ligands disappeared.
> >>
> >> How can I get pymol to display the ligands as well?
> >>
> >> Here is in detail.
> >>
> >> As you suggested, I created a new model by combining #1 and #10, and
> saved the newly single model in a PDB file. However, when I displayed this
> file in pymol, I could not see the ligand as shown in the figure.
> >> <image.png>
> >> <image.png>
> >> So we tried to align the ligand OSW-1 to the protein osh4 in this
> figure, but it was difficult to analyze because OSW-1 was far away from the
> distance of the protein osh4 as shown in the figure below.
> >>
> >> <image.png>
> >>
> >>
> >> Refernece：Save command:
> >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb>
> >>
> >> Also, I've looked at tutorials and other sites on the Internet to try
> to figure out what's causing this, but no luck!
> >>
> >> I'm sorry for the many questions.
> >>
> ---------------------------------------------------------------------------
> >> 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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>
>
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