On Wednesday 29 March 2006 02:48, Paul Pillot wrote: > Water molecule is flat, and should be represented by Jmol. It's the > first model I use with my students to show the basics of molecular > visualisation. I would not like to have it rotating in one plane only.
Not really. 2D coordinates are defined not as 'flat', but as having only XY defined. 3D coordinates have XYZ. MDL molfiles are tricky in this respect, because the use the same syntax for 2D and 3D coordinates. Another reason to use semantically rich formats, like CML. > Some more complex chemical structures are also flat (some steroids, > nucleic bases (?not sure of the translation),...). > It would be hard to discriminate. This is exactly the reason... flat in 3D should mean, flat. if we would draw 3D geometries 2D in Jmol, it indicates that it is flat and hence hard to discriminate. > I strongly agree with what has been said : let's the authors taking the > responsability of their use of Jmol. Authors responsibilities has given *a lot of* pain in chemoinformatics; it leads to ad hoc solutions. 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&kid=110944&bid=241720&dat=121642 _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
