Hi, >I am interested in your thoughts and feedback. Since you asked...
We always deal with changes in languages that break existing code. The problem is that Rasmol/Jmol/etc., are always going to meeting this as you enhance your respective code bases with new features. Clearly the confusion that this generates means it must get 'fixed' in such a way that it is clear to everyone who is interested in it that the rotations be 'consistent'. There probably is no way to identify what the script author intended. Therefore it will hard to know whether or not a script has been broken. Thus, it is up to the author or user to change them. This puts me off option 3 because someone may use a combination of options. For example, loading one old script and then load a new script within the same session without a step to change compatibility modes creates the error. This is likely to be very common in teaching. Also, you may end up with multiple flags that confuses the heck out of the inexperienced user and you either tend to forget what flags to use or don't understand which flags to use. So I would opt for option 2 because I think it is far better to break existing scripts if that make everything 'consistent' than have confusion. Regards Bruce ---- Original message ---- >Date: Tue, 17 Feb 2004 01:37:23 +0100 (CET) >From: Miguel Howard <[EMAIL PROTECTED]> >Subject: RasMol rotations about axes >To: [EMAIL PROTECTED], [EMAIL PROTECTED] > >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. > >Should Jmol be 100% RasMol/Chime compatible? >Should Jmol only support a fully right-handed system? >Can't we have both? > > >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 > >The general feeling from the jmol-users seems to be that we should offer >the option of having +Y go up and +Z come out of the screen. Many think >that this is a more natural orientation that is adopted by math >textbooks, OpenGL, VRML, etc. > > > >Now, we need to talk about the rotations. > >As I understand it, a right-handed rotation should be counter-clockwise >when the viewer is positioned on the + axis and is looking towards the >origin. > >To visualize it with your hand ... > - with your right hand > - extend your thumb > - curl your fingers > - point your thumb at your nose > - you are looking at the origin from the + end of the axis > - your fingers are pointing in the direction of the rotation > >I believe that this is consistent with Anthony Stone's previous email to >jmol-users. > >Let's look at the axis rotations in RasMol ... > > load someMolecule > set axes on > rotate x 10 > >You then need to take the mouse and wiggle it a little. I observe that >the +Z axis (which is in the back) comes up. > >Point your thumb to the right with your fingers curled. The fingers are >curling up from the back. This means that RasMol did a right-handed >rotation around the X axis. Good. > >Let's skip to the Z axis > > reset > rotate z 10 > >I observe that the +X drops on the right. The +Z axis goes into the >screen. Point your right thumb into the screen. Your fingers are curling >down on the right. RasMol is doing a right-hand rotation around the Z >axis. Good. > >Finally, let's look at the Y axis > > reset > rotate y 10 > >I observe that the +Z axis at the back moves to the left. The +Y axis >points down, so point your right thumb down. Fingers are curling around >back to the *right* ... but +Z moved to the *left*. Huh? > >Try it with your left hand. Thumb down, fingers curl to the left, +Z >moved to the left ... it sure looks like to me that RasMol is doing a >left-hand rotation around the Y axis. > > > >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 :-) > >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. > >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 > > 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 > > 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? > > > >I am interested in your thoughts and feedback. > > >Thanks, >Miguel > > > >----------------------------------------------------------------rasmol-+ > >To change your address, unsubscribe, view previous messages/history, >receive messages as weekly digests, or for any other information >about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > >----------------------------------------------------------------rasmol-- > ------------------------------------------------------- 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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