On Saturday 08 October 2005 11:30, FyD wrote: > Quoting Egon Willighagen <[EMAIL PROTECTED]>: > > On Saturday 08 October 2005 09:33, FyD wrote: > > > With the corresponding CML file converted from a Tripos file: > > > http://www.u-picardie.fr/labo/lbpd/jmol-10.00/Test/MeOH.cml > > > > Very good! > > > > I'm happy to see that you took this approach. BTW, how did you convert > > the file? Did you indeed make a custom script, or did you use OpenBabel? > > With R.E.D. http://www.u-picardie.fr/labo/lbpd/RED/, we automatically > derive RESP and ESP charges using GAMESS|Gaussian and RESP. I just added a > new routine in R.E.D.-III to generate automatically .xml files using the > optimized Cart. coord obtained from the QM soft output and the RESP-ESP > charges from RESP output. R.E.D. builds .mol2 using the same idea...
That's even better... to have native CML support. There are a few CML tweaks I can suggest though: ===================================================== <?xml version="1.0"?> <molecule xmlns="http://www.xml-cml.org/schema/cml2/core"; xmlns:jmol="http://www.jmol.org/";> <!-- added the namespaces so that we (and the processing software) know what syntax we're dealing with --> <atomArray> <atom id="a1" elementType="C" x3="0.6555" y3="-0.0197" z3="0.0000"><scalar dictRef="jmol:charge">0.1687</scalar></atom> <atom id="a2" elementType="H" x3="1.0766" y3="0.9760" z3="0.0000"><scalar dictRef="jmol:charge">0.0234</scalar></atom> <atom id="a3" elementType="H" x3="1.0129" y3="-0.5434" z3="0.8835"><scalar dictRef="jmol:charge">0.0234</scalar></atom> <atom id="a4" elementType="H" x3="1.0129" y3="-0.5434" z3="-0.8835"><scalar dictRef="jmol:charge">0.0234</scalar></atom> <atom id="a5" elementType="O" x3="-0.7370" y3="0.1206" z3="0.0000"><scalar dictRef="jmol:charge">-0.6652</scalar></atom> <atom id="a6" elementType="H" x3="-1.1399" y3="-1.1399" z3="0.0000"><scalar dictRef="jmol:charge">0.4262</scalar></atom> </atomArray> <bondArray> <bond atomRefs2="a1 a2" order="S"/> <bond atomRefs2="a1 a3" order="S"/> <bond atomRefs2="a1 a4" order="S"/> <bond atomRefs2="a1 a5" order="S"/> <bond atomRefs2="a5 a6" order="S"/> </bondArray> </molecule> ===================================================== E. -- [EMAIL PROTECTED] PhD student on Molecular Representation in Chemometrics Radboud University Nijmegen http://www.cac.science.ru.nl/people/egonw/ GPG: 1024D/D6336BA6 ------------------------------------------------------- This SF.Net email is sponsored by: Power Architecture Resource Center: Free content, downloads, discussions, and more. http://solutions.newsforge.com/ibmarch.tmpl _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
