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