[Jmol-developers] Re: Jmol coordinate system

[Miguel H. <mt...@mt...>]

> Miguel,
>
> I loaded the same small-molecule pdb file into three programs, pymol,
> crystalmaker, and jmol-appplet. The first two displayed the image the
> same way but jmol displays it with the y-coordinate going down rather
> than up so I had to rotate the molecule 180 deg about x to get identical
> views. Shouldn't jmol have an axes system with (from the bottom left
> corner) X pointing to the viewers right, Y pointing up and Z coming out
> of the screen?
>
> Richard

I had completely forgotton about this issue.
Actually, I had mentally *blocked* this issue because it is so annoying.

The quick answer is:

We need to expose a setting that would give users control over the axis
orientation.


The longer answer is:

RasMol/Chime use a *different* coordinate system. And one of the goals of
Jmol is to provide a migration path for existing RasMol/Chime educational
material. So, about 6 months ago, I changed Jmol to adopt the RasMol
coordinate system of orientations and rotations.

You can see the axes with the script command
  set axes on

or by checking the checkbox in the Display menu (in the Jmol application)


This affects the orientation of the X/Y/Z axes. That is the easy part.

I think the bigger problem is that it also affects the 'rotate z' script
command. I think that what I figured out was that the 'rotate z' script
command is actually left-handed. So we need to decide what to do about
this ... with advice from people who have existing scripts.


Miguel