On Wednesday 17 September 2003 14:41, Peter Murray-Rust wrote: > At 13:08 15/09/2003 +0200, Miguel wrote: > >My question regards the direction of the positive y axis of molecular > >model coordinates when rendered on the screen. > > (This relates to JChempaint but I think is worth crossposting). > > It is extremely important to get these right. In molecular structure > programs it is essential to get the handedness correct and these are both > right-handed as required. > > > JChempaint (and other editors must necessarily have Z OUT of the screen. > > ... continued ... > > On looking carefully at import and export from/to MDL molfiles to/from > Jchempaint it looks as if MDL: 2D software has an origin at lower left (x > l2r, y bottom2top) while JChempaint has 0,0 at upper left. This means that > not only is the diagram drawn "upside down" - which is much more important > for 2D than 3D **** BUT THE CHIRALITY IS REVERSED ****. > > Can others check that if this statement is true? If so it will be essential > to fix JCP asap or people will be corrupting structures.
Yes, it is true and filed on SourceForge as a bug ;) Gemma and I discovered the problem in August... Should JCP be fixed... i.e. the renderer? or the IO? Though JCP 2.x is still not stable we could change it... but files written with JCP 1.x and earlier JCP 1.9.x versions might be corrupted by the change... (just thoughts, not arguments...) Anyway, JCP, or actually the Renderer2D seems to violate the common editor handedness, right? So, that should be fixed... Everyone agrees? Egon ------------------------------------------------------- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
