huge thanks to d8vela / pymol_scripts

step 1: link .pymolrc anywhere else (aka home dir) to this pymolrc file

ln -s ~/scripts/python_scripts/pymol_scripts/pymolrc .pymolrc

step 2: set up alias in bashrc

alias pymol="/Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL $1" alias bam='pymol -d bam'

step 3: how to set up paths "/path/to/home/scripts/python_scripts/pymol_scripts"

add new pml scripts to pymolrc lines add python scripts into pymol_scripts followed by reference in --init--pymol doc