Hi, 

If I open a protein structure, change the right mouse to rotate, select the structure, rotate it by the right mouse, and then execute the following script in the Python Shell, the structure will be moved; see the video (https://i.gyazo.com/d72344f9c8610298f574c23e53224aac.mp4). I would expect it to be not moved as the mol.atoms.coords have not been changed. The mol.atoms.scene_coords have been changed instead. But this could be my misunderstanding of the design intent. I encounter some bugs in the downstream analysis using scene_coords only. 

from chimerax.atomic import Structure
mol = session.models.list(type = Structure)[0]
transformation = mol.scene_position
mol.atoms.transform(transformation)

However, if I open the same structure again and execute the following, it will go to the user's rotation. 

mol_2 = session.models.list(type = Structure)[1]
mol_2.atoms.transform(transformation)

So, I then applied the following code in my script. As a result, everything is as expected, and there is no bug. 

mol_path = mol.filename
transformation = mol.scene_position
mol.delete()
mol = run(self.session, f"open {mol_path}")[0]
mol.atoms.transform(transformation)

I wonder if there is a way to bypass this re-opening of the file. I am with version 1.7.1 (2024-01-23) on Win 11. 

Many thanks, 
Roden





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