Dear Angel, Thanks for your reply. It was a stupid error in the input file. I've assumed that atom coordinates are given in unit cell coordinates and used SCALEn keyword to get a normal representation. Obviously, Jmol ignores this keyword in PDB file and as far as atoms are too close to each other Jmol draws bonds between all of them. After I've scaled the coordinates manually the error disappeared.
You are right, the versions of Jmol and applet were different. Best regards, Pavel >Hello Pavel > >I can imagine no reason for Jmol application and applet to behave >differently. > >1. Are they the same version? > >2. You can disable autobonding using a command (although that should >affect both app and applet). That command can go in the page source >or in the pdb file itself >http://chemapps.stolaf.edu/jmol/docs/#set_autobond >http://wiki.jmol.org/index.php/File_formats/Scripting#Script_inline_wi >thin_a_molecular_coordinates_file > >3. If you share the file or the url, I'll gladly have a look at it > >4. finally, you could draw lines between atoms instead of using bonds ------------------------------------------------------------------------------ AppSumo Presents a FREE Video for the SourceForge Community by Eric Ries, the creator of the Lean Startup Methodology on "Lean Startup Secrets Revealed." This video shows you how to validate your ideas, optimize your ideas and identify your business strategy. http://p.sf.net/sfu/appsumosfdev2dev _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
