Dear Miguel,
I think you are right. Once again, the best fix would be a
command line switch. Changing the default would break lots
of scripts.
Clearly Jmol is an independent program and its developers
can do whatever they think best, but with over a million
existing rasmol users worldwide, providing them with
a program that works in a similar fashion when they are
using a browser might be a good idea.
Regards,
Herbert
=====================================================
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY, 11769
+1-631-244-3035
[EMAIL PROTECTED]
=====================================================
On Tue, 17 Feb 2004, 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.
>
> 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
>
>
>
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