The problem of ligands disappearing when the file is converted
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: image.png] [image: 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: 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@st.go.tuat.ac.jp
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:
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:
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@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@st.go.tuat.ac.jp
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@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@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@st.go.tuat.ac.jp
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@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@st.go.tuat.ac.jp
2021年12月21日(火) 3:24 Elaine Meng meng@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@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@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@st.go.tuat.ac.jp
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (2)
-
Elaine Meng -
Kenji MATSUI