My question regards the direction of the positive y axis of molecular model coordinates when rendered on the screen.
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.
RasMol/Chime render the positive y axis going down (and positive z axis going away from the user and into the screen)
Jmol renders the positive y axis going up (and positive z axis coming out of the screen and towards the user)
This is problematic since I am trying to provide a smooth migration path from Chime to Jmol ... I assume that I will put in a user option.
What do other molecular visualization programs do?
ACD /3D appears to have +z INTO the screen Weblab ViewerLite has z OUT of the screen Mercury CCDC has Y INTO the screen
JChempaint (and other editors must necessarily have Z OUT of the screen.
So I doubt there is any real agreement other than the axes must be right-handed. Personally I would have the origin at bottom left (e.g. RasMOL-like)
P.
Miguel
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