Thanks for your question.
flag ignore, atom-selection, set
Will enable you to remove the surface from selected atoms. For example:
flag ignore, resn wat or resi 150, set
Warren L. DeLano, Ph.D.
DeLano Scientific LLC
> -----Original Message-----
> From: pymol-users-admin@... [mailto:pymol-users-
> admin@...] On Behalf Of michael lerner
> Sent: Wednesday, September 24, 2003 11:03 AM
> To: pymol-users@...
> Subject: [PyMOL] drawing the surface correctly
> 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
> 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.
> 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, 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
> 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
> be able to do this all within PyMOL. My ligand is named NAP, so I
> "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
> alter the file, save it and reload it, PyMOL displays the surface
> 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.
> michael lerner
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