1) > Does anyone every go into the code to see what really happening when > Jmol/JSmol parsing the JME format, cuz the JME format works > incredible well for the limited information containing in the JME > format.
The relevant source must be in http://chemapps.stolaf.edu/jmol/jsmol/j2s/J/adapter/readers/simple/Jme Reader.js as compared to http://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/src/org/jmol/a dapter/readers/simple/JmeReader.java 2) Are you comparing JSmol to a recent version of Jmol (ideally the same version). I say so because formerly Jmol used the UFF force field for 3D minimization, while more recently MMFF94 became available. There might be a difference there in performance. 3) > When the molecule in MOL format passes onto JSmol, it works fine with > no EM. Note that when you transfer MOL data into Jmol, EM will (or may) be run too, to generate the 3D. When JME is passed that is automatic, since JME is really one-dimensional (text string) data, not 2D as MOL is. 4) > Even so I still am trying to address the problem using mol format, as > the charge information (the number of H atoms) in the mol file is not > presented right in JSmol. I have always had problems with 3-bonded carbons as Jmol refuses to add a H to them (assuming they are sp2 which is often not the case). Not sure if that's related to your problem. There may be a limitation in dealing with charged atoms when calculating Hs. Or the charge field is not being recognized. · Dr. Angel Herráez Biochemistry and Molecular Biology, Dept. of Systems Biology, University of Alcalá E-28871 Alcalá de Henares (Madrid), Spain ------------------------------------------------------------------------------ Android is increasing in popularity, but the open development platform that developers love is also attractive to malware creators. Download this white paper to learn more about secure code signing practices that can help keep Android apps secure. http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
