>Miguel said
>
>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.
You are perfectly correct.
Rotation about x and z is right-handed.
Rotation about y is left-handed
This is true for *all* versions of RasMol/Chime I have
tested.
>Q: Please post some independent confirmations telling
me that you >concur ...or explaining my error :-)
I have tested this with the rotate command for the
following programs, taking care *not* to be confused
by incorrect labelling of Y in some versions.
RasWin 2.6beta2a (incorrect y axis labelling)
RasWin 2.7.2.1 (incorrect y axis labelling)
RasMol 2.7.2.1 linux (correct y axis labelling)
It is also confirmed by the following description in
the RasMol Manual/Help File. Just do the appropriate
gesticulating and head scratching ;-)
--------------------------------------------------------------------
Rotate
Syntax: rotate <axis> {-} <value>
Rotate the molecule about the specified axis.
Permitted values for the axis parameter are x, y and
z. The integer parameter states the angle in degrees
for the structure to be rotated. For the X and Y axes,
positive values move the closest point up and right,
and negative values move it down and left
respectively. For the Z axis, a positive rotation acts
clockwise and a negative angle anti-clockwise.
---------------------------------------------------------------------
>Q: I have not tried this in Chime ... can someone
check it out and
>confirm that it behaves the same way?
Chime Pro 2.6 SP4 behaves exactly the same as the
RasWin versions above (also with incorrect Y axis
labelling).
>Q: Can someone also confirm that the chime 'move'
command about the y >axis is also left-handed?
Correct again.
For Chime Pro 2.6 SP4 the chime move command about the
x and z axes is right-handed, and about the y axis is
left-handed
>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 propagated
> - 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
Personally, I favour 2 - combined with a lucid
explanation in Jmol documentation and a wild, on-line,
script-fixing party which sorts out the issue
once-and-for-all. But then, I�ve got no real scripts
to fix.
> 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?
If required, why not go for a single �chime
compatibility switch� (off by default) that deals with
axis orientation, rotation and any other Chime
anomalies which appear?
How about �chime on� / �chime off� or �set chime on� /
�set chime off�?
Regards
Geoff
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