Hi Thomas, Joel gave some pointers using the menus. But the reason for giving spheres and mentioning that as a generic way is that spheres will work for connected as well as non-bonded atoms. In the case of sulphate you probably want to have a stick representation. The hydrogen bonds can be drawn using the 'distance' command. See
http://www.pymolwiki.org/index.php/Displaying_Biochemical_Properties Cheers, Tsjerk On Fri, Mar 27, 2009 at 8:19 AM, Jhon Thomas <jhon1.tho...@gmail.com> wrote: > Hello Tsjerk > > > Thanks for your reply... > > I want to show my ligand (sulpahete) in my figure and its interaction with > the selcted atoms of the selected residues (Hbonds, ionic etc). as well as i > want to show the interaction (hbonds) with the selected atoms of the > selected residues. shwing sphere wouldnot be a good way. i will appreciate > your help. > > Thank you > > Thomas > > On Thu, Mar 26, 2009 at 12:45 AM, Tsjerk Wassenaar <tsje...@gmail.com> > wrote: >> >> Hi Thomas, >> >> You're not really specific here, so I'll give the most general reply: >> >> show spheres, hetatm >> >> By the way, these compounds will definitely be drawn either as sticks >> or as nonbonded upon loading of the structure. You may not easily see >> them, but if they're in the file, they'll be drawn. >> >> Hope it helps, >> >> Tsjerk >> >> On Wed, Mar 25, 2009 at 5:30 PM, Jhon Thomas <jhon1.tho...@gmail.com> >> wrote: >> > Hi all >> > >> > I would like to know, how we can show the ligands in pymol. Although i >> > can >> > see the non-bonded atoms ( HOH) automatically, eacept other nonbonded >> > atoms >> > l;ike sulphate and metal ions. I will appreciate the suggestions. >> > >> > Thanks in advance >> > >> > Thomas >> > >> > >> > >> > >> > ------------------------------------------------------------------------------ >> > >> > _______________________________________________ >> > PyMOL-users mailing list >> > PyMOL-users@lists.sourceforge.net >> > https://lists.sourceforge.net/lists/listinfo/pymol-users >> > >> > >> >> >> >> -- >> Tsjerk A. Wassenaar, Ph.D. >> Junior UD (post-doc) >> Biomolecular NMR, Bijvoet Center >> Utrecht University >> Padualaan 8 >> 3584 CH Utrecht >> The Netherlands >> P: +31-30-2539931 >> F: +31-30-2537623 > > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623
