Re: [Jmol-users] Ligands
Basically it is just Select ligand Robert M. Hanson Chair, Chemistry from my Windows phone -Original Message- From: "J. Bays" Sent: 3/30/2016 4:53 PM To: "jmol-users@lists.sourceforge.net" Subject: Re: [Jmol-users] Ligands Yes. Thanks. I am working on something for our biochemist. J. Philip Bays Emeritus Professor of Chemistry Saint Mary's College Norte Dame, IN Sent from my iPad > On Mar 30, 2016, at 5:44 PM, Otis Rothenberger wrote: > > Phil, > > I’m a little molecule guy, but see if this page has what you want: > > http://chemapps.stolaf.edu/pe/protexpl/htm/seleccmd.htm > > Otis > -- > Otis Rothenberger > o...@chemagic.org > http://chemagic.org > >> On Mar 30, 2016, at 4:30 PM, Philip Bays wrote: >> >> Can JSmol pick out and display ligands in proteins? What is the script for >> that? >> >> Phil >> >> Philip Bays >> Emeritus Professor of Chemistry >> Saint Mary's College >> Notre Dame, IN 46556 >> pb...@saintmarys.edu >> >> >> >> -- >> Transform Data into Opportunity. >> Accelerate data analysis in your applications with >> Intel Data Analytics Acceleration Library. >> Click to learn more. >> http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140 >> ___ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users > > > -- > Transform Data into Opportunity. > Accelerate data analysis in your applications with > Intel Data Analytics Acceleration Library. > Click to learn more. > http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140 > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Ligands
Hi Phil Several ways of picking ligands -- depends a little on your definition which is not always what Jmol understands by "ligand" You can do select ligand but that may not match all that you expect. It's a synonym for not protein and not nucleic and not water Particularly, my experience is that the major problem is with isolated nucleotides like GTP, which are seen as nucleic by Jmol and so not included in ligand. I think there was a trick to look for single-residue nucleics, but I will need to dig it out. Aha, I put it here: http://wiki.jmol.org/index.php/AtomSets#By_type_of_molecule Good luck. Let me know if I can help further -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Ligands
Yes. Thanks. I am working on something for our biochemist. J. Philip Bays Emeritus Professor of Chemistry Saint Mary's College Norte Dame, IN Sent from my iPad > On Mar 30, 2016, at 5:44 PM, Otis Rothenberger wrote: > > Phil, > > I’m a little molecule guy, but see if this page has what you want: > > http://chemapps.stolaf.edu/pe/protexpl/htm/seleccmd.htm > > Otis > -- > Otis Rothenberger > o...@chemagic.org > http://chemagic.org > >> On Mar 30, 2016, at 4:30 PM, Philip Bays wrote: >> >> Can JSmol pick out and display ligands in proteins? What is the script for >> that? >> >> Phil >> >> Philip Bays >> Emeritus Professor of Chemistry >> Saint Mary's College >> Notre Dame, IN 46556 >> pb...@saintmarys.edu >> >> >> >> -- >> Transform Data into Opportunity. >> Accelerate data analysis in your applications with >> Intel Data Analytics Acceleration Library. >> Click to learn more. >> http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140 >> ___ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users > > > -- > Transform Data into Opportunity. > Accelerate data analysis in your applications with > Intel Data Analytics Acceleration Library. > Click to learn more. > http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140 > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Ligands
Phil, I’m a little molecule guy, but see if this page has what you want: http://chemapps.stolaf.edu/pe/protexpl/htm/seleccmd.htm Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Mar 30, 2016, at 4:30 PM, Philip Bays wrote: > > Can JSmol pick out and display ligands in proteins? What is the script for > that? > > Phil > > Philip Bays > Emeritus Professor of Chemistry > Saint Mary's College > Notre Dame, IN 46556 > pb...@saintmarys.edu > > > > -- > Transform Data into Opportunity. > Accelerate data analysis in your applications with > Intel Data Analytics Acceleration Library. > Click to learn more. > http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140 > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Ligands
Can JSmol pick out and display ligands in proteins? What is the script for that? Phil Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
