Hi Angel, Thank you for the reply.
In http://bdb4.ucsd.edu/bind/surflex.jsp?PDB=1GSI&HET=TMP, the multi layer means one protein (as model=1.1), one crystal ligand (as model=2.1), and the other ligands (as model=3). 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${hmap.url}-results.mol2";, "set frank off", "model 0", "select model=1.1; spacefill off; cpk off; wireframe off; cartoon; color cartoon translucent; zoom 200", "select model=2.1; wireframe 80; spacefill 0.35; center hetero; color translucent; zoom 200", "select model=3; wireframe off; cpk off; spacefill off", "background white", "display all" ]; jmolInitialize("/bind/jmol-13.0.18/",true); jmolApplet( 600, jmolcmds.join(";"), "${pdb}" ); jmolBr(); I agree that single protein behaves nicely at http://bdb4.ucsd.edu/bind/jmol_pdb.jsp?pdbid=1GSI&monomerid=50332929&polymerid=p50000494&seq=100&title=pound34Thymidylate%20kinasepound34%20AND%20pound34CHEMBL394429pound34. But did you try http://bdb4.ucsd.edu/bind/surflex.jsp?PDB=1GSI&HET=TMP. I would like jmol show the protein in http://bdb4.ucsd.edu/bind/surflex.jsp?PDB=1GSI&HET=TMP as protein displayed in http://bdb4.ucsd.edu/bind/jmol_pdb.jsp?pdbid=1GSI&monomerid=50332929&polymerid=p50000494&seq=100&title=pound34Thymidylate%20kinasepound34%20AND%20pound34CHEMBL394429pound34 Thank you in advance. PS. the two are posted again http://bdb4.ucsd.edu/bind/jmol_pdb.jsp?pdbid=1GSI&monomerid=50332929&polymerid=p50000494&seq=100&title=pound34Thymidylate%20kinasepound34%20AND%20pound34CHEMBL394429pound34 http://bdb4.ucsd.edu/bind/surflex.jsp?PDB=1GSI&HET=TMP ------------------- All the best to you, Tiqing Liu, Ph. D. ________________________________________ Message: 1 Date: Thu, 22 Aug 2013 20:22:55 +0200 From: Angel Herr?ez <[email protected]> Subject: Re: [Jmol-users] Help please To: <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="US-ASCII" Hello Liu Can you be more specific? That would help. By "multiple layer", do you mean several models (frames) are loaded together? Or something else? > http://bdb4.ucsd.edu/bind/surflex.jsp?PDB=1GSI&HET=TMP does not behave where not all the atoms and bonds in protein are cartooned. Which parts of the protein are not displayed? I just loaded the pdb into Jmol and I see no problem in the cartoon. Finally, this will not affect, but for your information you do not need to repeat "set appendNew true", and "zoom" applies to all models at the same time, so no need to repeat it. ------------------------------------------------------------------------------ Introducing Performance Central, a new site from SourceForge and AppDynamics. Performance Central is your source for news, insights, analysis and resources for efficient Application Performance Management. Visit us today! http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
