-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Tuesday 17 February 2004 01:37, Miguel Howard wrote: > Summary > ======= > I may be wrong on this, so I need people to check my work ... > > It looks to me like the RasMol rotations about axes are not consistently > right-handed. > > We need to discuss this and try to figure out what to do about it ... if > anything ... whether or not it is something we need to *fix* in Jmol. > > The bad news is that changing the rotation behavior would break every > script that uses the 'rotate y <degrees>' command or the Chime 'move' > command. The good news is that the repair is quite easy.
Good. > Should Jmol be 100% RasMol/Chime compatible? Compatible, but not in bugs... I've been following the discussion with interest, but did not have time to respond earlier. Do I see things right that when displaying a right-handed coordinate set in a left-handed ccordinate system will invert stereochemistry ? So we need to ask ourselves: is the coordinate system in file formats left or right handed... and Jmol should follow that instead of RasMol/Chime... (I think right handed cartesian is normally used). > Should Jmol only support a fully right-handed system? > Can't we have both? I got a bit confused by the hand descriptions, and I think my thumb, index and middle finger are not flexible enough to support but systems, so I think I can follow it a bit... but isn't a normal cartesian system not always one of those? Being right-handed cartesian.... If so, aren't files always using this one system? If so, Jmol should do only one system too? (Or maybe switch to the other, if some weird file format supports the other coord system...) > Detail > ====== > I think we have the general understanding that the axis orientation in > RasMol is right-handed. With the default orientation of having > - +X to the right > - +Y going down > - +Z into the screen I think that is a correct RH system. <snip> > I have looked at this several dozen times over the past 6 months. At > first I wasn't confident of my observations, but now I have convinced > myself. But I may be wrong ... I certainly have struggled with this > 'handedness' stuff :-) > > Q: Please post some independent confirmations telling me that you concur > ... or explaining my error :-) Using a right-handed cartesian system is important. I don't have special feelings what a positive rotation is about... being compatible with the latest Rasmol/Chime seems sensible then... > Q: I have not tried this in Chime ... can someone check it out and > confirm that it behaves the same way? > > Q: Can someone also confirm that the chime 'move' command about the y > axis is also left-handed? > > Unfortunately, this has pretty big implications for someone who has a > large investment in existing scripts (Eric?). It means that all moves and > rotates around the Y axis need to be negated. At least it isn't difficult. > > My goal for Jmol has been to get as close as possible to 100% RasMol/Chime > script compatibility, to ease the migration path for people who have > existing scripts. But this might be a pretty big change for people who > have an investment in tutorials/courseware. It may be a bit blunt, but I think we should not be compatible up to the bug level just to keep tutorial one-to-one convertable... > As I see it, the options are pretty similar to the Axis Orientation > question: > > 1. Jmol should only support RasMol/Chime rotations > - people have made an investment in existing > RasMol/Chime scripts > - it works fine, leave it alone > - people are used to seeing it behave this way > - it doesn't really matter, no one has looked > at it for years so nobody really cares Agreed. > 2. Jmol should be completely right-handed > - the system should be consistently right-handed > - the fact that y rotates backwards is a design > flaw that should be corrected, not propogated > - people have been confused by this for years > - noone is going to use existing scripts anyway > - OR, those who have scripts can easily change them > - OR, just write a script converter that will > fix existing scripts ... just negate the parameter > to 'rotate y <degrees>' and 'move x <Y> z ...' > commands More importantly, it should be right-handed or otherwise we will mess up stereochemistry... if these bugs are found in some Rasmol/Chime versions, did no one ever notice the unnatural proteins? > 3. Jmol should offer both > - it is easy to support both > Q: What should the default orientation be in Jmol? > Q: What should the script command be to change > the setting? > Q: Is this *exactly* the same switch that controls > the Y axis orientation? Jmol should not offer both left-handed and right-handed. I think all file formats are right-handed. Getting the stereochemistry right is a life issue (literally!). Getting the stereochemistry wrong of medicine can lead to very dangerous situations... (Was the problem with DES not like this?) > I am interested in your thoughts and feedback. Egon - -- [EMAIL PROTECTED] PhD on Molecular Representation in Chemometrics Nijmegen University http://www.cac.sci.kun.nl/people/egonw/ GPG: 1024D/D6336BA6 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.7 (SunOS) iD8DBQFAMcynd9R8I9Yza6YRAp1IAJ9BvqCAEItzPUPqe4Sh05BBHyHOtwCfZ3uE 9vFH3xMDh69o+aDH0hEuzmU= =ZoSr -----END PGP SIGNATURE----- ------------------------------------------------------- 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. 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