Hi Nir, Pymol just draws bonds based on distances, not based on topological information. If atoms are within contact distance, a bond will be drawn, whatever the atoms are. If one feels need for an additional bond, it is possible to add them using:
bond selection1, selection2 This will draw bonds between all atoms of selection1 and all atoms of selection2. In Thierry's case it would be something like: bond resi X and resn asp and name CD, resi Y and resn lys and name NZ assuming this is about a side chain - side chain amide bond. Hope it helps, Tsjerk On Tue, Mar 31, 2009 at 9:14 PM, Nir London <n...@rosettadesigngroup.com> wrote: > Hi, Can anyone help thierry ? > http://rosettadesigngroup.com/blog/10/pymol-scripts/#comment-3149 > " I would like to ask to make a special bond in pymol. Actually in my > protein I have a real covalent bond between an Asn and a Lys.. Obviously, > Pymol doesn’t know how to draw it. Can you help me ? > Thanks. " > thierry > > Nir London. > Rosetta Design Group. > http://rosettadesigngroup.com/blog/ > ------------------------------------------------------------------------------ > > _______________________________________________ > 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
