>-----Original Message----- >Message: 7 >Date: Thu, 5 Feb 2004 20:34:34 +0100 (CET) >From: "Miguel Howard" <[EMAIL PROTECTED]> >To: <[EMAIL PROTECTED]> >Subject: [Jmol-users] rasmol axes orientation >Reply-To: [EMAIL PROTECTED]
>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? (No one ever sees these things, so >maybe it doesn't really matter) Yes I care :-) I have also noticed (what I think is) the same inconsistency in RasMol. For me it was evidenced in the display of the show axes command. From memory (I don't have RasMol in front of me) The X and Z axes are correctly labelled (in the positive direction) but the Y axis is labelled at the wrong end (in the negative direction). Hence my money is on Y being wrong. I also suspect that this is why unit cells are drawn in 'unexpected' places by RasMol/Chime. >Q: Is right-handed good enough, or are there people/groups who want a >left-handed system? Er... Not sure about this >Q: Do people agree that the rotation commands should be consistent with >the axes orientation? (right-hand implies counter-clockwise rotations) I'm all for consistency. For me, one of the delights of Jmol is that it actively addresses and resolves these problems. 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
