The purpose of this memo is to start a discussion about an 'issue' with axis orientation.
I don't think it is that important for the biochemists, but I suspect it will be more important for the crystalographers. As far as I can tell, the combination of axis orientation and rotation commands in RasMol/Chime is *wrong* ... it is neither left-handed nor right-handed, but a mix. Let me explain. The x & y axes are pretty straightforward. For the x axis, increasing values go to the right. And for the y axes, increasing values go up. No problems. But the positive Z axes goes into the screen and away from the viewer. This would seem to imply that the system is left-handed. However, the rotations are not left-handed. - when looking at the origin from the positive x axis rotations are counter-clockwise - when looking at the origin from the positive y axis rotations are clockwise - when looking at the origin from the positive z axis rotations are counter-clockwise (I may be mistaken on one of these, but I am quite confident that one of the three is different). In order to maintain compatibility with existing RasMol/Chime scripts, I felt compelled to switch the orientation of the JmolAxes to comply with RasMol/Chime. However, I do not feel good about this and want to provide a smooth upgrade path for those who prefer to work with a clean & consistent system. I think this will also avoid some of the orientation problems that occur when someone exports from another molecular modeling package. (There is, in fact, a check-box on the pop-up menu which allows you to choose the axis orientation ... because I felt so bad about it.) My proposal is to expose a command that would switch the entire system to right-handed ... both the axes orientation and the rotations. Q: Does anyone actually care about this? (Noone ever sees these things, so maybe it doesn't really matter) Q: Is right-handed good enough, or are there people/groups who want a left-handed system? Q: Do people agree that the rotation commands should be consistent with the axes orientation? (right-hand implies counter-clockwise rotations) Miguel ------------------------------------------------------- The SF.Net email is sponsored by EclipseCon 2004 Premiere Conference on Open Tools Development and Integration See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. http://www.eclipsecon.org/osdn _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
