[Jmol-developers] [Cdk-devel] y coordinate orientation

[Peter Murray-R. <pm...@ca...>]

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).

PMR ...

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.

P.