Hi Peter, In order to do this you either need to extract the ligand to its own object or unset the ignore flag on "rep surface". That is,
# fetch the protein fetch 1rg7, async=0 # show surface show surface, resn MTX # do not ignore surfacing of ligands flag ignore, not rep surface # force PyMOL to rebuild the surface rebuild Cheers, -- Jason On Sat, Apr 2, 2011 at 12:22 PM, Peter C. Kahn <k...@aesop.rutgers.edu> wrote: > Dear All, > > Is there a way to show the surface of a ligand? In the file 1RG7 > dihydrofolate reductase has the inhibitor methotrexate bound in the > active site. S surface yields the surface of the protein but not of the > inhibitor, which remains as lines. The command 'select MTX, resn MTX' > followed by S spheres for the MTX selection yields the van der Waals > representation. How can I show the solvent accessible surface of the > inhibitor? > > (It is easier to see the problem if you color the whole protein one > color, e.g. magenta, and then color the methotrexate yellow.) > > Is this a general problem for ligands? > > Thanks, > > -- > Peter C. Kahn, Ph.D. > Professor of Biochemistry > Department of Biochemistry& Microbiology > Rutgers University > 76 Lipman Drive > New Brunswick, NJ 08901 > > Telephone: 732-932-9255, ext. 120 > Telefax: 732-932-8965 > Email: k...@aesop.rutgers.edu > > > ------------------------------------------------------------------------------ > Create and publish websites with WebMatrix > Use the most popular FREE web apps or write code yourself; > WebMatrix provides all the features you need to develop and > publish your website. http://p.sf.net/sfu/ms-webmatrix-sf > _______________________________________________ > 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 ------------------------------------------------------------------------------ Create and publish websites with WebMatrix Use the most popular FREE web apps or write code yourself; WebMatrix provides all the features you need to develop and publish your website. http://p.sf.net/sfu/ms-webmatrix-sf _______________________________________________ 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
