Bob,
I may not understand what should be happening here, so I'll be a bit
more specific.
> It's suppose to load with the same orientation to the viewer that the
> user left it in when saved with Spartan. Is it not doing that? Rotate
> the model in Spartan, save it, and load it into Jmol. Doesn't it
> appear the same as how you saved it? Jmol is supposed to be reading
> the orientation from the Spartan file and reproducing that.
>
Using benzene as an example, the Spartan (.spartan) appears to be
loading the coordinates below which I've copy/pasted from the .spartan
file via a text reader. The model was recorded in the XZ plane, and Jmol
is rendering it in the XZ plane. If I do an axes on, the X axis is
perpendicular to the screen.
If I use Jmol to capture the molfile of this same model (also pasted
below) and load this molfile, the rendering now has the Z axis
perpendicular to the screen, but the model is in the YZ plane. There has
been a coordinate swap.
Both renderings are correct per the data, but the axes have been
swapped. Is what I've described expected behavior?
Otis
SPARTAN PROPERTIES PACKAGE: MAC/P4 build 129c
Use of molecular symmetry enabled
Molecular charge: 0
Spin multiplicity: 1
Electrons: 30
Cartesian Coordinates (Angstroms)
Atom X Y Z
--------- ------------- ------------- -------------
1 H H1 0.0000000 0.0000000 -2.4946974
2 C C1 0.0000000 0.0000000 -1.3950414
3 C C4 0.0000000 0.0000000 1.3950414
4 C C2 -1.2081412 0.0000000 -0.6975207
5 C C6 1.2081412 0.0000000 -0.6975207
6 C C5 1.2081412 0.0000000 0.6975207
7 C C3 -1.2081412 0.0000000 0.6975207
8 H H2 -2.1604714 0.0000000 -1.2473487
9 H H6 2.1604714 0.0000000 -1.2473487
10 H H5 2.1604714 0.0000000 1.2473487
11 H H3 -2.1604714 0.0000000 1.2473487
12 H H4 0.0000000 0.0000000 2.4946974
http://localhost:8080/meps/benzene.txt
Jmol version 12.1.11_dev 2010-09-05 20:18
MODELKIT: ({0:11})
12 12 0 0 0
0.0 2.494697 0.0 H
0.0 1.3950412 0.0 C
0.0 -1.395041 0.0 C
0.0 0.6975206 -1.208141 C
0.0 0.6975206 1.2081412 C
0.0 -0.697520 1.2081412 C
0.0 -0.697520 -1.208141 C
0.0 1.2473484 -2.160471 H
0.0 1.2473484 2.1604712 H
0.0 -1.247348 2.1604712 H
0.0 -1.247348 -2.160471 H
0.0 -2.494697 0.0 H
1 2 1
2 5 6
5 6 7
3 6 6
3 7 7
4 7 6
2 4 7
6 10 1
7 11 1
3 12 1
4 8 1
5 9 1
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