Sorry, Tiqing, but I do not see what the problem is. The proteins in those two pages
http://bdb4.ucsd.edu/bind/jmol_pdb.jsp?pdbid=1GSI&monomerid=50332929&polymerid=p50000494&seq=100&title=pound34Thymidylate%20kinasepound34%20AND%20pound34CHEMBL394429pound34

and
> http://bdb4.ucsd.edu/bind/surflex.jsp?PDB=1GSI&HET=TMP

look similar to me.
What is the defect you are seeing?

Also, as I said in my former message, "select model=1.1" is OK, but  "select model=3" does not work. You need "select 3.0" or "select file=3" to select all 3 models in that file. Maybe that is the origin of the problem.

Try to change to:


  var jmolcmds = [ "load http://bdb4.ucsd.edu${hmap.url}.pdb ",
  "set appendNew true",
  "load APPEND http://bdb4.ucsd.edu${hmap.url}_ligand0.mol2 ",
  "load APPEND http://bdb4.ucsd.edu${hmap.url}-results.mol2 ",
  "set frank off",
  "model 0",
  "select 1.1; spacefill off; cpk off; wireframe off; cartoon; color cartoon translucent",
  "select 2.1; wireframe 80; spacefill 0.35; center hetero; color translucent; zoom 200",
  "select 3.0; wireframe off; cpk off; spacefill off",
  "background white",
  "display all"
 ];