Dear All, I use Jmol to visualize CML files within HTML pages. These CML files are generated from Tripos mol2 files. This means that the CML files do countain the connectivities between the atoms.
If you look at http://www.u-picardie.fr/labo/lbpd/REDDB/uploadfile/F-56/info.html The second molecule "Fragment RA5" (for instance) presents a connection problem and a bond which should not exist is created. See the corresponding file @ http://www.u-picardie.fr/labo/lbpd/REDDB/uploadfile/F-56/tripos2.mol2.cml 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. I can understand that Jmol calculates its own connectivities based on atom distances in the absence of connectivity information, 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 ? Thanks, regards, 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 [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
