Hi folks I have now experimented with a few different versions of RasMol and think I have got a coherent explanation/answer to the problem of axes orientation
I modified a 2x2x2 unit cell lithium pdb file to display a 'reference' set of labelled axes using 'dummy atoms'. Since these directly relate to the X Y Z atom coordinates in the pdb file they should be correct. For this particular cubic lithium structure the X Y and Z axes are also coincident with the A, B, and C 'edges' of the unit cell. I have linked this pdb file to http://moodle.yeovil.ac.uk/~geoffr/ so that others can view and test this. (Use the script 'select 0' followed by 'label %c' to label the 'dummy atom' axes; then compare this to 'set axes on') 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). However, the Windows versions of RasMol (2.6 beta2a or 2.7.2.1) display the Y axes pointing in the wrong (negative) direction. For the Windows version of Rasmol 2.6beta2a 'set unitcell on' draws the unit cell in an 'unexpected' location displaced in the negative Y direction. Windows RasMol (2.7.2.1) seems to be a partial 'fix' in that it does draw the unitcell in the expected position. I have not directly tested it, but from previous experience I am fairly sure that Chime has inherited the Windows RasMol 2.6 behaviour. To summarise, this all indicates that the way Jmol displays the axes is correct and is consistent with the Linux version of RasMol. The Windows versions of RasMol that I have tested, and Chime, are wrong. Note that 'show axes' in my earlier posting should have read 'set axes on' (oops dodgy memory !) Hope this helps to clear things up - rather than adding to the complexity! Regards Geoff -----Original Message----------------- Message: 3 Date: Thu, 5 Feb 2004 20:36:03 -0500 From: timothy driscoll <[EMAIL PROTECTED]> Subject: Re: [Jmol-users] rasmol axes orientation To: [EMAIL PROTECTED] Reply-To: [EMAIL PROTECTED] at 8.34p EDT on 2004 February 05 Thursday Miguel Howard said: > The purpose of this memo is to start a discussion about an 'issue' with > axis orientation. >=20 > I don't think it is that important for the biochemists, but I suspect it > will be more important for the crystalographers. >=20 well, as one of the former, I'll add my $0.02. I would much prefer a consistent and unambiguous axis orientation - that is= , either left or right handed. it would be ideal if Jmol followed convention= s established in other software, as well (I don't know how most other softwar= e behaves in this regard, but maybe others will). but I also agree with your approach because... > 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. >=20 =2E..I think this is a valuable feature. > My proposal is to expose a command that would switch the entire system to > right-handed ... both the axes orientation and the rotations. >=20 > Q: Does anyone actually care about this? (Noone ever sees these things, s= o > maybe it doesn't really matter) >=20 A: it depends. if I were to send a move command, then the command to switc= h the axes orientation, then run the same move command... the result of the t= wo moves would be different, right? which means that by using the proposed command, I could mess up animation scripts imported from Chime. but as long as the Chime behavior remains an option for now (not necessaril= y the default, btw), I am in favor of such a command. it can be set before a Chime animation is imported. > Q: Is right-handed good enough, or are there people/groups who want a > left-handed system? >=20 A: I'm left-handed, so... actually, no I don't care one way or the other. :-) > Q: Do people agree that the rotation commands should be consistent with > the axes orientation? (right-hand implies counter-clockwise rotations) >=20 yes, this person does. regards, :tim --=20 timothy driscoll molvisions - molecular graphics & visualization <http://www.molvisions.com/> usa:north carolina:wake forest ------------------------------------------------------- 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
