>> Correct. If no connectivity information is presented then Jmol will >> calculate connectivity. > > OK > >> > but I would expect Jmol to follow the connectivities >> > if the list of connections is provided in the CML file >> > (and not to add new ones). >> > >> > Am I wrong ? >> >> You are correct. The rule is that if connectivity information is present >> in the file then Jmol will respect that connectivity and will not add >> any >> more bonds. > > The problem is that Jmol adds two new bonds _besides_ the list of > connectivities already available in the CML file...
Jmol will not do that. The problem is: * the connectivity information in the CML file is invalid * the file reader discards all of the invalid bond records * there is no connectivity information in the file * Jmol calculates *all* of the connectivity > See: http://www.u-picardie.fr/labo/lbpd/REDDB/uploadfile/F-56/info.html > & > http://www.u-picardie.fr/labo/lbpd/REDDB/uploadfile/F-56/tripos2.mol2.cml Nico is correct. The atomRefs must contain references to atom ids. There is no concept of atom number. You have this: <atom id="O3'" elementType="O" x3="-3.505024" y3="-1.071412" z3="1.676940"><scalar dictRef="jmol:charge">-0.5387</scalar></atom> <atom id="P" elementType="P" x3="-4.285099" y3="-2.041241" z3="0.839733"><scalar dictRef="jmol:charge">1.2162</scalar></atom> ... <bond atomRefs2="1 2" order="1"/> You need this: <bond atomRefs2="O3 P" order="1" /> Miguel ------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=lnk&kid3432&bid#0486&dat1642 _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
