Michael,
Thanks for your question.
flag ignore, atom-selection, set
rebuild
Will enable you to remove the surface from selected atoms. For example:
show surface
flag ignore, resn wat or resi 150, set
rebuild
Cheers,
Warren
--
mailto:warren@...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -----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
>
> 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
>
>
>
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