I tried to set up a web page using chemdoodle sketcher as a molecule drawing tool, in association with Jmol. Chemdoodle sketcher is a pure javascript toolkit but it reads an exports mol files. All works quite well (my draft in progress can be accessed at http://librairiedemolecules.education.fr/outils/scribmol/), except when I draw a carbon attached to 3 other carbons (and not four). The Following Mol file is issued by chemdoodle sketcher : Molecule from ChemDoodle Web Components
http://www.ichemlabs.com 5 4 0 0 0 0 999 v2000 -0.8660 -1.0000 0.0000 C 0 0 0 0 0 0 -0.0000 -0.5000 0.0000 C 0 0 0 0 0 0 0.8660 -1.0000 0.0000 C 0 0 0 0 0 0 -0.0000 0.5000 0.0000 C 0 0 0 0 0 0 0.8660 1.0000 0.0000 C 0 0 0 0 0 0 1 2 1 0 0 0 2 3 1 0 0 0 2 4 1 0 0 0 4 5 1 0 0 0 M END After transferring to Jmol, the minimize addhydrogens command doesn't add any hydrogen to the carbon linked to the other 3. The three bonds are set as planar. I tried with the Avogadro software and it does add an hydrogen to this carbon, and after minimization the bonds are set as in a tetrahedron. Am I missing something here, or is there a problem in the way Jmol add hydrogens to carbons in that specific case ? For information, I tried to draw the same formula with Otis's JMEtoJmol web page, and did not notice the same problem (but I think the communication to JME does not obey to the same conversions) -Paul PS : thanks to Angel for is inspirational DIY page ------------------------------------------------------------------------------ Storage Efficiency Calculator This modeling tool is based on patent-pending intellectual property that has been used successfully in hundreds of IBM storage optimization engage- ments, worldwide. Store less, Store more with what you own, Move data to the right place. Try It Now! http://www.accelacomm.com/jaw/sfnl/114/51427378/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
