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.
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.
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.
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Kenji Matsui
Graduate School of Tokyo University of Agriculture and Technology
2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan