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
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