Hello, I've investigating to see how a ligand interacts with a channel protein and visualizing it in PyMOL. Here's how it looks when I load two .pdbqt files: one for the channel protein and the other for ligand (turquoise). I call this ligand "original".

When I save the channel & ligand as a .pdb file into 1 object and load that file again in PyMOL. The ligand is truncated (yellow).

And this is what it looks like when I overlay the "original" and the "different" ligand.

Here are the settings that I saved the molecule with. I haven't encountered this issue when I loaded other ligands into the channel and saving them as a .pdb file.

When I checked the "Write HEADER for every object" option and exported then load the .pdb file into PyMOL again. It displays the ligand in the channel correctly, though they are separate objects.

When I try to merge these two separate objects into 1 using the "create" PyMOL command and export it as a .pdb file and open it again. Then the ligand is truncated again. I'm not sure why this is happening.