> Per my previous e-mail, I have a Windows solution that works (free MDL > Chime plug-in).
If you are happy with Chime then you should use it. > The file I sent you is properly displayed by this plug-in > even in 3D. I have added preliminary test code to Jmol which supports the V3000 format. I did not realize that you file was 2D until I tested your file. I am not very familiar with Chime. I do not know what Chime's behavior is when it reads a 2D .mol/.sdf file. Jmol will treat it as a 3D molecule where all the Z coordinates are 0.0 ... just as it is written in the file. This presents problems with files that do not have connectivity information because the distances are incorrect, causing problems for the 'autobond' code. In addition, some 2D files store coordinates as integer pixel counts ... which Jmol interprets as angstroms. These do not seem to be problems in the sample file that you sent. There is a connection table and the distances look reasonable. I have been told by several experts that this is not a good way to represent 2D data, because it can give the wrong impression that the molecule is flat. That is the primary reason why I suggested that you may want to consider a proper 2D viewer. I have some questions about the format ... The sample file contains more than one molecule in the file ... Q: What is the proper behavior if more than one molecule is present in the file? Q: What does Chime do? Miguel ------------------------------------------------------- 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
