On Wednesday 22 March 2006 14:19, Hervé Azoulay wrote: > Sorry to resend this question that might seem a very minor issue to all of > you but that is becoming pretty critical for me now. I've tried to open > V3000 structure with JMOL version 10 and still have the same error message > "No atoms in file". I think the file (attached here) is correct since I can > open it with other (MDL) tools. > > I had a look to the source code and if I'm correct, there is a V3000Format > class but the CDK V3000Reader class is missing in the JMOL 10 distribution. > What I would like to know is whether I'm right or wrong and if using JMOL > is or will be soon a possibility for me.
CDK indeed has a v3000 reader, but Jmol does not. You should either start Jmol such that it uses the CDK reader: java -Dmodel=cdk -jar Jmol.jar (which only works in Jmol 10) Otherwise, file a feature request on the Jmol website for a v3000 MDL molfile reader. I might have time this weekend to write one for Jmol. Egon -- [EMAIL PROTECTED] PhD student on Molecular Representation in Chemometrics Radboud University Nijmegen Blog: http://chem-bla-ics.blogspot.com/ http://www.cac.science.ru.nl/people/egonw/ GPG: 1024D/D6336BA6 ------------------------------------------------------- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid0944&bid$1720&dat1642 _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
