Geoff, > This displays the Jmol +X +Y +Z labels entirely coincident with > the 'dummy atom axes' > > If you rotate this so that X points to the left, and Y points > up, then Z points out of the screen, towards the user
My understanding is that this is *not* a right-handed system, it is a left-handed system. To be right-handed you want +X to the right, +Y up and +Z out of the screen. > 4 Finally select 'Jmol Unit Cell' which places the unit cell > 'between' the positive XYZ axes - exactly where I would expect it to > be. I agree that is where Jmol puts them when it is in 'axes compatibility mode'. > I have just noticed that if I right click the applet window the > 'Axes Rasmol/Chime' option is selected (ticked) on the menu. > > If I clear this, so that 'Axes Rasmol/Chime' is not ticked, the > structure 'shifts' but when rotated has the same handedness i.e. when X > points to the left, and Y points up, then Z points out of the > screen. > > So I am not sure what the 'Axes Rasmol/Chime' option is doing? This option returns Jmol to a right-handed coordinate system ... or at least what *I* think is a right-handed system. (Note that I do not think that this setting is currently affecting rotations and moves ... as it should) > I get exactly the same behaviour when using Internet Explorer or > Mozilla on Windows 98 or XP or using Mozilla on Redhat Linux 9 (just > trying to eliminate any other variables!). Good ... we better not find any difference across platforms :-) > In my hands a recent Linux version of (Open)RasMol(2.7.2.1 16BIT > version) also displays the axes using 'set axes on' in the same way. > > I think this is the 'correct' way and should be the default for > Jmol. Note that I have not tried any scripts involving 'rotation' or > 'handedness' so do not have any experience of how this fits. > > However, I agree with you that both the Windows version of > RasMol 2.6 beta 2a and Chime have the Y axis labelled by 'set axes on' > pointing in the 'wrong' direction i.e. into the screen, if X > points to the left and Y up. I think we need to double check this ... I believe that RasMol 2.7 is consistent with RasMol 2.6 and Chime. > My feeling is that Jmol should use the 'correct' (i.e. not > Chime) axes orientation and that if this causes problems with > scripts, then these should be edited. If this is not trivial, then I > see why an option to mimic Chime behaviour would be useful. However > this does not seem to be implemented in this version of the Jmol > applet. > > Am I totally missing the point here, or otherwise going mad? I > would be grateful if anyone can clarify this. Uhhh ... no comment :-) Let's start by agreeing on what a right-handed system is ... then we will go from there. 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
