Hi Nir, If you have the structure of the small molecule, why not try the following:
load yourProtein.pdb load yourSmallMol.pdb create complex, * The new object called "complex" will now have the protein and small molecule. If you don't--and want something for illustration only--then you can convert it from SMILES to pdb using lots of different software. After this, you can throw it into a docking program and use the output for your image. Again, I stress "for illustration only." Cheers, -- Jason On Thu, May 6, 2010 at 11:57 PM, Nir Qvit <nir.q...@gmail.com> wrote: > Hi, > Is there is a way to add a small molecule to a protein after loading a > pdb file of the protein from the database? > We are trying to make a figure of a protein and a small molecule that we > know that is interacting with the protein. In the database there is the > structure of the protein only. > What will be the best way to add the small molecule to the protein for a > schematic figure? > thanks for your help, > Nir > > Nir Qvit, Ph.D. > Postdoctoral Fellow > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > 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 ------------------------------------------------------------------------------ _______________________________________________ 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
