Francois wrote: > This means that the CML files do countain the > connectivities between the atoms. [snip] > 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. > 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. (Note that PDB files are an exception to this rule, because the PDB specification calls for optional CONECT records that specify connectivity in addition to the 'normal' bonds.) Regarding your issue Francois ... I have been doing some work to allow people to use scripting commands to add and delete specific bonds. This functionality will allow you to explicitly select the *incorrect* bond and delete it. I plan to release this code within a week. So you may want to test this new functionality before you go to the trouble of adding connectivity to your CML files. 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
