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%20kinasepou
nd34%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"
];
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