>> These 'dummy atom' axes are completely consistent with those displayed >> by 'set axes on' in the Jmol applet and the Linux version of RasMol >> (2.7.2.1 16BIT version). These have the correct handedness i.e. with >> the X axis pointing to the right, the Y axis pointing up, and the Z axis >> pointing out of the plane of the screen towards the user. Also, 'set >> unitcell on' draws the unit cell in the same, expected, location for >> both Jmol and RasMol (Linux). >Geoff, >Hmmm ... I do not believe that Jmol has this axis orientation. I believe >that Jmol has the Z axis pointing away from the user ... to be consistent >with RasMol 2.6 beta 2a. >I am travelling right now and further discussion will have to wait.
>Miguel Miguel et al. Whenever you get the opportunity, take a look at http://moodle.yeovil.ac.uk/~geoffr/Li_axes/Li_axes_Jmol.htm This is using the unitcell-enabled beta version of the Jmol applet which you recently emailed to me. Try for example: 1 select 'Hide atoms' 2 select 'Dummy atom XYZ Axes showing origin (O) and positive X,Y,Z vectors This should display XYZ axes encoded by dummy atoms in the PDB file 3 select 'Jmol XYZ' Axes 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 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 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? 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!). 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. 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. Regards, Geoff ------------------------------------------------------- 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_id56&alloc_id438&op=click _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
