Hi Mark, The surface representation of a protein, in PyMol, shows the "Connolly" surface or the surface that would be traced out by the _surfaces_ of waters in contact with the protein at all possible positions. Also, since PDBs don't have hydrogens, and PyMOL will calculate the surface for whatever is present, you should add and render surfaces for a protein with hydrogens. I think this will give you the most biophysically relevant representation for you published image.
Cheers, -- Jason On Mon, Jun 28, 2010 at 6:46 PM, Mark A Saper <sa...@umich.edu> wrote: > If a model is modified, the "rebuild" command does not always update the > surface. For example, > > show lines, theProtein and not elem H > show surface > > show lines, elem H > rebuild > > The surface does not change. But if I now, > > hide surface > show surface > > the surface swells slightly to account for the hydrogens. > > Is this a bug? or a feature? Also, is it appropriate to show surfaces in > publication in the presence of the H's? Or does the 1.4 Å probe sphere that > PyMOL uses intended to account for them? > > Mark > _________________________________ > Mark A. Saper, Ph.D. > Associate Professor of Biological Chemistry > University of Michigan > sa...@umich.edu phone (734) 764-3353 fax (734) 764-3323 > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
