Bob,
As you might suspect, I am not at all disappointed to hear that it's
Spartan's fault!
This all has to do with an append load of these files into the same
frame. I move the initial model in the XY plane to get it out of the
way. Then I append a second file. With Spartan, I end up with a user
confusing Z displacement of the models. If Tom can't make Spartan
behave, I guess I can write a separate routine for Spartan files with an
initial YZ displacement. Fortunately, we keep these things in a separate
load menu.
Thanks for checking.
Otis
Otis Rothenberger
chemagic.com
On 9/16/2010 3:45 PM, Robert Hanson wrote:
Otis,
Isn't that interesting!!! I had not noticed that.
Jmol is taking the output geometry, not the input geometry, from the
Spartan file. For example, for benzene in that C6H6.smol file on the
website,we have:
BEGININPUT
OPT HF 3-21G FREQ
benzenevib
0 1
1 0.000000000 0.000000000 -0.020393968
6 0.000000000 0.000000000 1.075605989
6 0.000000000 0.000000000 3.847966909
6 0.000000000 -1.200467944 1.768697023
6 0.000000000 1.200466990 1.768695951
6 0.000000000 1.200467944 3.154876947
6 0.000000000 -1.200466990 3.154876947
1 0.000000000 -2.149631739 1.220696926
1 0.000000000 2.149630785 1.220695972
1 0.000000000 2.149631739 3.702876925
1 0.000000000 -2.149630249 3.702877820
1 0.000000000 0.000000000 4.943966866
ENDCART
...
ENDINPUT
But Jmol skips those and uses instead the final coordinates:
BEGINMOLSTATE
MODEL=3~HYDROGEN=1~LABELS=0
-0.00000004 -0.00000004 1.00000000 0.00000000
-0.99999994 0.00000000 -0.00000004 0.00000000
0.00000000 -0.99999994 -0.00000004 0.00000000
0.00000000 0.00000000 0.00000000 1.00000000
ENDMOLSTATE
BEGINVIBSTATE
ENDVIBSTATE
BEGINCELLS
ENDCELLS
BEGINARCHIVE
External AB INITIO PROGRAM: converted archive file
Jobname.Temp
12 66 30 54 0 1 66 0 RHF 3-21G(d) NOOPT FREQ
GEOMETRY
1 4.6433727 0.0000000 0.0000000
6 2.6168992 0.0000000 0.0000000
6 -2.6168992 -0.0000000 0.0000000
6 1.3084496 2.2663012 0.0000000
6 1.3084496 -2.2663012 0.0000000
6 -1.3084496 -2.2663012 0.0000000
6 -1.3084496 2.2663012 0.0000000
1 2.3216863 4.0212787 0.0000000
1 2.3216863 -4.0212787 0.0000000
1 -2.3216863 -4.0212787 0.0000000
1 -2.3216863 4.0212787 0.0000000
1 -4.6433727 -0.0000000 0.0000000
(Those are atomic units.) Beats me why they do the coordinate switch.
But Jmol certainly isn't doing that, Spartan is.
Bob
On Thu, Sep 16, 2010 at 12:23 PM, Otis Rothenberger
<[email protected] <mailto:[email protected]>> wrote:
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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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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