Rick, I briefly spoke with Egon on irc today. He has been very busy, but said that he would answer your questions regarding CML and crystals this weekend.
Miguel > I'm doing my best to answer my own question regarding CML files with > periodic information. > > I attach a CML file for Si/diamond that *does* work with JMOL. I did > lots of trial and error and have found several inconsistencies between > the CML reference and what works in Jmol. I raise these issues here not > to in any way diminish the excellent behavior of the Jmol application > (and the CDK library!), but in the hope that I can help fix these > problems. > > 1. The CML reference I found > (http://www.xml-cml.org/dtdschema/cmlCore/HTMLDOCS/) says that > <crystal> records need to have a,b,c,alpha,beta, and gamma values > specified as <scalar> fields. By looking at the estron.cml file in the > samples directory, which does load properly, it seems that the lattice > needs to be loaded as a matrix, e.g. > <crystal> > <floatArray convention="PMP" title="a" >10.200 0 0</floatArray> > <floatArray convention="PMP" title="b" >0 10.200 0</floatArray> > <floatArray convention="PMP" title="c" >0 0 10.200</floatArray> > </crystal> > I have no idea what convention="PMP" does, but it appears to be > necessary. > > 2. The CML reference also states that atoms may be described using > xFrac="0.25" yFrac="0.25" zfrac="0.25" descriptions rather than the > corresponding x3,y3,z3 specifications. I have not found that fractional > coordinates work. Oddly enough, I also haven't been able to get > xyz3="0.0 0.0 0.0" type modifiers of atoms to work either. > > 3. <bond> tags don't seem to work for crystals. > > Once again, I'm grateful that an application with the ease of use and > power of Jmol exists. I'd be glad to look into these bugs (I should > probably join the Jmol-developers email list), but there may be already > people who can track this problem down in less time. > > I attach a working Si/diamond structure. > > Rick Muller > [EMAIL PROTECTED] -------------------------------------------------- Miguel Howard [EMAIL PROTECTED] c/Pe�a Primera 11-13 esc dcha 6B 37002 Salamanca Espa�a Spain -------------------------------------------------- telefono casa 923 27 10 82 movil 650 52 54 58 -------------------------------------------------- To call from the US dial 9:00 am Pacific US = home 011 34 923 27 10 82 12:00 noon Eastern US = cell 011 34 650 52 54 58 6:00 pm Spain -------------------------------------------------- ------------------------------------------------------- This SF.net email is sponsored by: SF.net Giveback Program. SourceForge.net hosts over 70,000 Open Source Projects. See the people who have HELPED US provide better services: Click here: http://sourceforge.net/supporters.php _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
