Otis, can you send me some Spartan files? I don't have Spartan set up yet.
Take something recognizable like a steroid and rotate it to various
directions in Spartan, then save the orientations as files under different
names and send them to me. I'd like to see how that looks. If you can send
me a snapshot of what each looked like in Spartan just before you saved the
file, that would be great.
Thanks,
Bob
On Thu, Sep 16, 2010 at 3:17 PM, Otis Rothenberger <[email protected]>wrote:
> 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 Rothenbergerchemagic.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]
> > 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
>
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.http://p.sf.net/sfu/novell-sfdev2dev
>
>
> _______________________________________________
> Jmol-users mailing
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>
>
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
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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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and start using them to simplify application deployment and
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