[PyMOL] Ligand surface

[Peter C. K. <kahn@AESOP.Rutgers.edu>]

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:      ka...@ae...