Fixes to visualization module

[zhang-ivy]

Description

Make fixes to the visualization module related to:

• Pymol frames are 1-indexed, but the module had been assuming it was 0-indexed
• Bug: self._unique_old/new should be self._unique_old/new_selection
• Renaming an object after loading isn't working, so instead, just load the objects as old and new directly
• Allow color of old residue to be different from the color of the new residue
• Change background protein transparency
• Remove "hide spheres" when we are using stick representation (shouldn't be necessary)
• Do not allow stick/sphere transparencies to fade to transparency 1.0 (completely transparent) -- make the max transparency 0.7, as there are weird visual artifacts when it is 1.0 (the stick/sphere looks white)
• Clarifications to comments/docstrings

Motivation and context

Resolves #???

How has this been tested?

Change log

[codecov]

Codecov Report

Merging #944 (3658e83) into main (9beb9b0) will decrease coverage by 0.91%.
The diff coverage is 0.00%.

[jchodera]

Thanks so much for improving this, @zhang-ivy!