Hi Ali,
I would typically use a temporary object for that, which is loaded into the
work space but never rendered:
def intra_rms_tempobj(filename):
from pymol import cmd
tmpname = cmd.get_unused_name('_tmpobj')
cmd.load(filename, tmpname, zoom=0)
try:
return cmd.intra_rms
I have noticed that PyMOL can be used to perform fast calculations by using it
in command line or through something like Jupyter notebook since it doesn’t
have to worry about the graphical geometries. I am curious if this can be
performed within the PyMOL program itself. For example, loading the
