On Tuesday 04 November 2003 11:22, Sebastian Lisken wrote: > Hi again, the recent discussion I joined was about .pdb files and > the "set connect" script command. Miguel said that when there is > bond information in a file, Jmol should stick to it, and I wonder > if this would apply to all formats. Back in the days of CaGe > development, the suggestion was made to indicate in a molecule > convention that the data should be taken "as is", even in the > case of "unchemical" molecules. > > I got a colleague who is still working with CaGe to send me two > samples of the CML format that I made our program send to the Jmol > applet. Note the "convention" in the third lines. I wonder what a > current version of the applet would make of them? What the display > should be with the "unchemical" file I don't know, I'm afraid - this > is not a question of the "what do you see" style but rather one > for the developers: what would Jmol make of the data in these > files, and would you be willing to make it adhere strictly to the > bonds and atom positions?
It looks like proper CML1... (and it is valid according to the CML1 DTD) So, it should work, but it is not... bonds are not read, so Jmol thinks the file does not have bonds... this is a bug in the CMLReader... I guess a similar thing is happening with the unchemical.cml... Can these two files be put in CVS for testing purposes? Egon -- [EMAIL PROTECTED] PhD on Molecular Representation in Chemometrics Nijmegen University http://www.cac.sci.kun.nl/people/egonw/ GPG: 1024D/D6336BA6 ------------------------------------------------------- This SF.net email is sponsored by: SF.net Giveback Program. Does SourceForge.net help you be more productive? Does it help you create better code? SHARE THE LOVE, and help us help YOU! Click Here: http://sourceforge.net/donate/ _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
