Jack,
What are all those extra "Q" atoms in the pdb file? They look to me like
compromise/placeholder coordinates for NMR-equivalent hydrogens...or something
like that.
To get a reasonable picture, you can get rid of the extra bonds with
unbond elem q*,all
or just nuke the "Q" atoms alto
Under linux does anyone else see the following? If one
loads in the 1pit.pdb from the MOLMOL data files, the
resulting structure seems to have extra bonds drawn in the
side chains. For example phe's seem to have all the opposing
carbons in the rings interconnected through the center of
the ring
