Hi Jianghai,
by default PyMOL does a distance based bonding (basically when the VDW
radii of two atoms overlap, they get connected). To prevent that, you
need two settings:
# before saving the correctly bonded but distorted structure
set pdb_conect_all
# before loading
set connect_mode, 1
I know this has come up before and I can't remember what the solution was.
PyMOL is drawing bonds between the protein I'm interested in, the ATP
analog, and the bound metal ions, presumably because the metals are close
enough to the protein and analog for bonds to be autodetected. Is there a
way
