On Friday 10 October 2003 18:33, Rick Muller wrote: > 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.
Yes, this is the old CML1 format I used myself. It's outdated... please use the the format of the CIF file Peter send. The v7 Jmol may be out of date with reading that file, but Jmol CVS can read it. And I'll try hard to release v8 this weekend. > 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. I'll make sure that v8 will parse your file properly if it is valid CML2. If it is not, I'll send you the changes you need to make, to make it valid... > 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), Yes, please fo. > but there may be already people who can track this problem down in > less time. Personally, speaking... I could fix issues with CML easily, but I have been very busy with writing papers/etc... (sorry for that) > I attach a working Si/diamond structure. Thanx. Egon -- PhD Molecular Representation in Chemometrics Laboratory of Analytical Chemistry http://www-cac.sci.kun.nl/people/egonw.html ------------------------------------------------------- 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
