> 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)
In an earlier (related) message you said:
>>RasMol/Chime render the positive y axis going down (and positive z axis >> going away from the user and into the screen) >Agreed
And I agreed with you.
So, it looks like that the MDL 2D software uses a different orientation from Chime. Am I understanding that correctly? They are not consistent within their product line.
I think it's fair to say that *all* 2D renderers use the same convention except for JChempaint. Because of this unanimity it has to be the "correct" orientation. The picture that JChempaint draws is a different chemical structure from everyone else and is "wrong" (i.e. any chemist looking at it would deduce the wrong stereochemistry).
All 3D renderers including Jmol seem to use right-handed axes and there is no apparent corruption of chirality. In general the actual orientation of the molecule on screen does not appear to matter to the community. If they output axes I would expect these to be oriented correctly wrt the molecule.
(Although I understand that, in some sense, they *inherited* the Chime code)
2D and 3D are completely different beasts. Relatively few systems manage them both together (CML does).
P.
Miguel
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