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
--
michael lerner
