I would like to restart the axis orientation discussion from the beginning.
I made several incorrect statements in the previous discussion and apologize for any confusion (or lewd hand gestures :-) that I may have caused. We are going to talk about orientation first ... rotations will be a separate discussion. Right Hand rule says that with the right hand: thumb -> +X index finger -> +Y middle finger -> +Z *Someone please confirm this* RasMol/Chime have the +X axis pointing to the right, the +Y axis pointing down, and the +Z axis pointing away from the user. This is a valid right-hand system. *Someone please confirm this* There is a switch on the popup menu called 'Axes RasMol/Chime'. This switch controls whether or not the +Y axis points down or up. By default, this switch is 'on', for RasMol/Chime compatibility. That means that by default, the +Y axis points down. If you uncheck this box, then the +Y axis points upwards. The molecule is (of course) rotated 180 degrees to reflect this. Whether this checkbox is checked or not, the Jmol axis orientation is always right-handed. *Someone please confirm this* My confusion surrounding this issue is caused by the fact that RasMol/Chime has the +Y axis pointing downwards. I find this orientation unnatural. Q: In the abstract, independent of any existing applications/scripts that may exist, what do people think about this? Do you believe that the +Y axis should point upwards or downwards? Q: Given that there *are* existing applications and tutorials, what do you think we should do about this issue? Q: Do other molecular visualization applications have the +Y axis pointing upwards or downwards? Miguel ------------------------------------------------------- SF.Net is sponsored by: Speed Start Your Linux Apps Now. Build and deploy apps & Web services for Linux with a free DVD software kit from IBM. Click Now! http://ads.osdn.com/?ad_id=1356&alloc_id=3438&op=click _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
