Thank you very mucho for your help! > The difficulty is defining the atoms involved in the receptor...showing > bonds and ribbons in the entire protein is quite easy: > > select protein; cartoon on; > > The ligand will display initially as bonds and atoms. I suspect this isn't > what you want :-) Here's script for displaying bonds and atoms only > within, > say, 6 Angstroms of the ligand(s): > > select protein; cartoon only; select within(6.0,ligand);wireframe 60; > spacefill 100; > > and if you're interested only in displaying sidechains: > > select protein; cartoon only; select within(6.0,ligand) and > sidechain;wireframe 60; spacefill 100; > > You can save that script to a .spt file for easy retrieval elsewhere (and > easy updating, if your fancy changes later), or you can just copy and > paste > it in the second argument of jmolApplet, just after "load > 1.1_1.1_1__receptor.pdb." > > Cheers, Mike > > On Wed, Mar 2, 2011 at 10:17 AM, <[email protected]> wrote: > >> Hello, i would like to find examples about how to define default values >> for a receptor-ligand model (pdb format). >> >> <script> >> jmolApplet(400, "load 1.1_1.1_1__receptor.pdb"); >> </script> >> >> For us is useful to load the applet showing "ribbons" and "bonds" for >> the >> receptor and "bonds" only for the ligand. >> >> Are any available Jmol example settings with receptor-ligand models? >> Thank you. >> >> >> >> ------------------------------------------------------------------------------ >> Free Software Download: Index, Search & Analyze Logs and other IT data >> in >> Real-Time with Splunk. Collect, index and harness all the fast moving IT >> data >> generated by your applications, servers and devices whether physical, >> virtual >> or in the cloud. Deliver compliance at lower cost and gain new business >> insights. http://p.sf.net/sfu/splunk-dev2dev >> _______________________________________________ >> Jmol-users mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> > > > > -- > Mike Evans > Organic Chemistry Graduate Student > Moore Group > University of Illinois, Urbana-Champaign > ------------------------------------------------------------------------------ > Free Software Download: Index, Search & Analyze Logs and other IT data in > Real-Time with Splunk. Collect, index and harness all the fast moving IT > data > generated by your applications, servers and devices whether physical, > virtual > or in the cloud. Deliver compliance at lower cost and gain new business > insights. http://p.sf.net/sfu/splunk-dev2dev > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users >
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