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:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of michael lerner > Sent: Wednesday, September 24, 2003 11:03 AM > To: pymol-users@lists.sourceforge.net > 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 > > > > ------------------------------------------------------- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
