[PyMOL] drawing the surface correctly

Howdy,

I have a pdb file that contains a protein, a ligand and two water 
molecules.  Everything in the protein is normal, and is listed with ATOM 
cards.  The ligand and waters are listed as HETATMs.  When I show the 
surface in PyMOL, I see the surface drawn around the protein only.  This 
is what I want. 

After I do some things to my protein in AMBER, I get a pdb file where 
everything is listed as an ATOM (it's a pretty simple pdb file .. ATOM, 
ATOM, ATOM, TER, ATOM, ATOM, TER, etc.).  When I load this into PyMOL 
and show the surface, the surface is drawn around the everything 
(ligand, water, and protein), rather than just around the protein.

If I open up the PDB file by hand and change all of the appropriate ATOM 
cards into HETATM cards and then load it up in PyMOL, everything works 
well (I see the surface drawn only around the protein).  But I'd like to 
be able to do this all within PyMOL.  My ligand is named NAP, so I type 
"alter resn NAP or resn WAT, type='HETATM'" followed by "sort" and 
"rebuild" to fix things.  Unfortunately, this doesn't work and I still 
get the surface drawn around everything.  The strange thing is that if I 
alter the file, save it and reload it, PyMOL displays the surface correctly.

Can I get PyMOL to display the correct surface without saving and 
reloading the file?

If it helps, I'm running PyMOL 0.90 on a Mandrake 8.2 laptop with an 
nVidia GeForce2Go graphics card.

Thanks,

-michael

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michael lerner