Quoting Miguel <[EMAIL PROTECTED]>: Oh oh, I am not sure you understood exactly what I wanted to say ;-)
I _do_ have a list a connectivities in the CML file... Please see: http://www.u-picardie.fr/labo/lbpd/REDDB/uploadfile/F-56/tripos2.mol2.cml > > I can understand that Jmol calculates its own connectivities based on atom > > distances in the absence of connectivity information, > > 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... 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 Details: The P(2) atom is linked to O(3) and H(20) to O(19) (this is normal), but for instance O(3) should _not_ be linked to H(20). I am aware that this structure presents an un-normal distance (too short) between those O(3) and H(20) atoms. Thanks, Francois ------------------------------------------------------- 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
