>>It is actually rotating as if the +Y axis is pointing upwards ... at >> least that is what it looks like to me. >> >>rotate x <degrees> & rotate y <degrees> behaved as I expected. > > Rotate should rotate the molecule relative to screen axes. The sign of > the rotation is critical. To determine that you must have ball and > stick or spacefill showing. If your Y axis is down the screen and you > apply a positive rotation I would expect the atoms nearest to you to > rotate leftwards and the ones farthest away to rotate rightwards. This > is a clockwise rotation about a Y axis down the screen.
I agree, that is what I expected.
What I observe in RasMols is that a positive rotation about the y axis: rotate y 20
moves the close atoms to the right and the far atoms to the left ... the opposite of what you describe.
I'd venture to suggest that Rasmol was "wrong". Rotations are usually clockwise in a righthanded sense. However this is an area where conventions can differ and one gets different results. I suspect (although Roger Sayle was a computer scientist) that this is unusual.
Having said this the normal graphics transformations are not related to screen axes. The default in many 3D systems seems to be to rotate the viewpoint about the object. It is a question of whether the matrix pre- or post- multiplies.
In the Jmol case it matters when one uses a script. It would be valuable to find other script-driven systems and see if they behave similarly. For mouse drag I would expect the rotation to move the nearer atoms in the direction of the drag.
P.
> It will help you to get a small molecule which you understand. It will > further help to make a physical molecular model. You can compare this > with what happens on the screen. In all cases it must be superimposable > with the screen molecule or you will have changed the chirality - not > allowed. If you don't have models use an orange with 4 cocktail sticks > and four atoms of different colours. Create a file for a molecule like > HC(F)(Cl)Br which is a tetrahedron. If you don't have that the > coordinates are > 1 1 1 > -1 -1 1 > 1 -1 -1 > -1 1 -1
Yes.
I have been using a 'molecule' with 7 unique atoms ... origin + unit vectors along the +/- axes. Nitrogen=North, Sulphur=South, Florine=Far, Carbon=Close, Oxygen=West (oueste in spanish), Chlorine=East (?), Hydrogen = origin
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