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
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