Hi Kenji,
I omitted your cxs file from this message since I thought maybe you wanted to keep it private (messages on this
chimerax-users@cgl.ucsf.edu mailing list can be seen by the public).
I didn't see that APBS error when I opened the cxs file in ChimeraX. It appears to be a message from another program (not ChimeraX): the APBS program, which calculates electrostatic potential. The error is exactly what it says: some residues in the structure are missing some atoms, which would affect the calculation of electrostatic potential values.
Short answer #1 is why not look at the interactions in ChimeraX instead of Pymol? You can calculate H-bonds, find contacts, etc. See this tutorial, for example
Short answer #2 is that you can open the session (cxs) file in ChimeraX and then save a PDB file with the "save" command or the menu: File... Save... (choose Files of type: PDB).
HOWEVER, a longer answer may be required here because I can see from opening your cxs file that it contains many models, I guess a receptor (model #1) and ligands from docking (models #2-258) with only some ligands displayed (models #10-17).
I'm guessing you want to save only the ones that are displayed. You could save models #1,10-17 into one multi-model PDB, file but probably for analysis in Pymol or other programs, you would instead need to combine each ligand with receptor and save it separately. In other words, you may need to make a new model by combining #1 with #10, and then save the new single model to a PDB file. For example:
combine #1,10 modelId #300
save /Users/meng/Desktop/result10.pdb models #300 relModel #1
Then repeat for other ligands, combining #1 with #11 to make a new model and saving that new model, combining #1 with #12, etc. See the help links below for the options of each command.
Save command:
Combine command:
I hope this helps,
Elaine
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Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco