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

[Kenji MATSUI]

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 at st.go.tuat.ac.jp
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