Subject: Normal Coordinate Visualisation

From: "Robert Fraczkiewicz" <[email-masked]>
Date: Wed, 14 Aug 1996 10:53:16 -0500

Dear Frederick,

>       I am wondering if anyone has a simple program for drawing normal
> coordinates on molecules once a frequency calculation has been done. Some
> nice graphics programs such as Spartan can animate the normal vibrational
> modes, but this is of little use for preparing static documents for example.
> I guess that something that could simply draw mass weighted cartesian
> coordinate arrows would be brilliant.
>
> Ciao

Molecular graphics program XMol available on variety of platforms from:

http://www.msc.edu/msc/docs/xmol/ftp.html

has a very nice "Extras/Animate" option that can do the trick. It can both
draw the arrows and animate normal modes. Since an example is the best teacher,
I am attaching one of the animation input files in XYZ format recognized by
XMol. This is one of the Ag vibrational modes of 6-atom (two Cu, two S and two
imidazoles as point masses) model of the active site of a metalloprotein known
as CuA. To see the arrows select "Display" menu and turn the option "Vectors"
on. To see animation select option "Animate" from "Extras" menu. The input
is composed of 30 frames in the following format

Atom_symbol  Atom_X Atom_Y Atom_Z  Arrow_X Arrow_Y Arrow_Z

You can manipulate relative arrow coordinates to make them longer or shorter.

Sincerely,
Robert Fraczkiewicz
University of Texas Medical Branch
Galveston, TX 77555
[email-masked]

-------------------------------CUT HERE-------------------------------------

            6
   2 Ag, Cu-63                      obs.  260.00 cm-1, calc.  260.17 cm-1
   CU     0.00000   0.00000   0.00000   0.09497  -0.06472   0.00000
   CU     2.47000   0.00000   0.00000  -0.09497   0.06472   0.00000
   S      1.23500   0.00000   1.79643   0.00000   0.00000   0.20062
   S      1.23500   0.00000  -1.79643   0.00000   0.00000  -0.20062
   N     -1.47847   1.24058   0.00000  -0.08343   0.06581   0.00000
   N      3.94847  -1.24058   0.00000   0.08343  -0.06581   0.00000
            6
   2 Ag, Cu-63                      obs.  260.00 cm-1, calc.  260.17 cm-1
   CU     0.01974  -0.01346   0.00000   0.07522  -0.05126   0.00000
   CU     2.45026   0.01346   0.00000  -0.07522   0.05126   0.00000
   S      1.23500   0.00000   1.83814   0.00000   0.00000   0.15891
   S      1.23500   0.00000  -1.83814   0.00000   0.00000  -0.15891
   N     -1.49582   1.25426   0.00000  -0.06608   0.05213   0.00000
   N      3.96582  -1.25426   0.00000   0.06608  -0.05213   0.00000
            6
   2 Ag, Cu-63                      obs.  260.00 cm-1, calc.  260.17 cm-1
   CU     0.03863  -0.02632   0.00000   0.05634  -0.03840   0.00000
   CU     2.43137   0.02632   0.00000  -0.05634   0.03840   0.00000
   S      1.23500   0.00000   1.87803   0.00000   0.00000   0.11902
   S      1.23500   0.00000  -1.87803   0.00000   0.00000  -0.11902
   N     -1.51240   1.26735   0.00000  -0.04949   0.03904   0.00000
   N      3.98240  -1.26735   0.00000   0.04949  -0.03904   0.00000
            6
   2 Ag, Cu-63                      obs.  260.00 cm-1, calc.  260.17 cm-1
   CU     0.05582  -0.03804   0.00000   0.03915  -0.02668   0.00000
   CU     2.41418   0.03804   0.00000  -0.03915   0.02668   0.00000
   S      1.23500   0.00000   1.91435   0.00000   0.00000   0.08270
   S      1.23500   0.00000  -1.91435   0.00000   0.00000  -0.08270
   N     -1.52751   1.27926   0.00000  -0.03439   0.02713   0.00000
   N      3.99751  -1.27926   0.00000   0.03439  -0.02713   0.00000
            6
   2 Ag, Cu-63                      obs.  260.00 cm-1, calc.  260.17 cm-1
   CU     0.07057  -0.04810   0.00000   0.02439  -0.01662   0.00000
   CU     2.39943   0.04810   0.00000  -0.02439   0.01662   0.00000
   S      1.23500   0.00000   1.94552   0.00000   0.00000   0.05153
   S      1.23500   0.00000  -1.94552   0.00000   0.00000  -0.05153
   N     -1.54047   1.28949   0.00000  -0.02143   0.01690   0.00000
   N      4.01047  -1.28949   0.00000   0.02143  -0.01690   0.00000
            6
   2 Ag, Cu-63                      obs.  260.00 cm-1, calc.  260.17 cm-1
   CU     0.08224  -0.05605   0.00000   0.01272  -0.00867   0.00000
   CU     2.38776   0.05605   0.00000  -0.01272   0.00867   0.00000
   S      1.23500   0.00000   1.97017   0.00000   0.00000   0.02688
   S      1.23500   0.00000  -1.97017   0.00000   0.00000  -0.02688
   N     -1.55072   1.29757   0.00000  -0.01118   0.00882   0.00000
   N      4.02072  -1.29757   0.00000   0.01118  -0.00882   0.00000
            6
   2 Ag, Cu-63                      obs.  260.00 cm-1, calc.  260.17 cm-1
   CU     0.09032  -0.06155   0.00000   0.00465  -0.00317   0.00000
   CU     2.37968   0.06155   0.00000  -0.00465   0.00317   0.00000
   S      1.23500   0.00000   1.98723   0.00000   0.00000   0.00982
   S      1.23500   0.00000  -1.98723   0.00000   0.00000  -0.00982
   N     -1.55781   1.30317   0.00000  -0.00408   0.00322   0.00000
   N      4.02781  -1.30317   0.00000   0.00408  -0.00322   0.00000
            6
   2 Ag, Cu-63                      obs.  260.00 cm-1, calc.  260.17 cm-1
   CU     0.09445  -0.06436   0.00000   0.00052  -0.00035   0.00000
   CU     2.37555   0.06436   0.00000  -0.00052   0.00035   0.00000
   S      1.23500   0.00000   1.99595   0.00000   0.00000   0.00110
   S      1.23500   0.00000  -1.99595   0.00000   0.00000  -0.00110
   N     -1.56144   1.30603   0.00000  -0.00046   0.00036   0.00000
   N      4.03144  -1.30603   0.00000   0.00046  -0.00036   0.00000
            6
   2 Ag, Cu-63                      obs.  260.00 cm-1, calc.  260.17 cm-1
   CU     0.09445  -0.06436   0.00000  -0.18942   0.12908   0.00000
   CU     2.37555   0.06436   0.00000   0.18942  -0.12908   0.00000
   S      1.23500   0.00000   1.99595   0.00000   0.00000  -0.40014
   S      1.23500   0.00000  -1.99595   0.00000   0.00000   0.40014
   N     -1.56144   1.30603   0.00000   0.16640  -0.13126   0.00000
   N      4.03144  -1.30603   0.00000  -0.16640   0.13126   0.00000
            6
   2 Ag, Cu-63                      obs.  260.00 cm-1, calc.  260.17 cm-1
   CU     0.09032  -0.06155   0.00000  -0.18529   0.12627   0.00000
   CU     2.37968   0.06155   0.00000   0.18529  -0.12627   0.00000
   S      1.23500   0.00000   1.98723   0.00000   0.00000  -0.39142
   S      1.23500   0.00000  -1.98723   0.00000   0.00000   0.39142
   N     -1.55781   1.30317   0.00000   0.16277  -0.12840   0.00000
   N      4.02781  -1.30317   0.00000  -0.16277   0.12840   0.00000
            6
   2 Ag, Cu-63                      obs.  260.00 cm-1, calc.  260.17 cm-1
   CU     0.08224  -0.05605   0.00000  -0.17721   0.12077   0.00000
   CU     2.38776   0.05605   0.00000   0.17721  -0.12077   0.00000
   S      1.23500   0.00000   1.97017   0.00000   0.00000  -0.37436
   S      1.23500   0.00000  -1.97017   0.00000   0.00000   0.37436
   N     -1.55072   1.29757   0.00000   0.15568  -0.12280   0.00000
   N      4.02072  -1.29757   0.00000  -0.15568   0.12280   0.00000
            6
   2 Ag, Cu-63                      obs.  260.00 cm-1, calc.  260.17 cm-1
   CU     0.07057  -0.04810   0.00000  -0.16554   0.11281   0.00000
   CU     2.39943   0.04810   0.00000   0.16554  -0.11281   0.00000
   S      1.23500   0.00000   1.94552   0.00000   0.00000  -0.34971
   S      1.23500   0.00000  -1.94552   0.00000   0.00000   0.34971
   N     -1.54047   1.28949   0.00000   0.14543  -0.11472   0.00000
   N      4.01047  -1.28949   0.00000  -0.14543   0.11472   0.00000
            6
   2 Ag, Cu-63                      obs.  260.00 cm-1, calc.  260.17 cm-1
   CU     0.05582  -0.03804   0.00000  -0.15079   0.10276   0.00000
   CU     2.41418   0.03804   0.00000   0.15079  -0.10276   0.00000
   S      1.23500   0.00000   1.91435   0.00000   0.00000  -0.31854
   S      1.23500   0.00000  -1.91435   0.00000   0.00000   0.31854
   N     -1.52751   1.27926   0.00000   0.13246  -0.10449   0.00000
   N      3.99751  -1.27926   0.00000  -0.13246   0.10449   0.00000
            6
   2 Ag, Cu-63                      obs.  260.00 cm-1, calc.  260.17 cm-1
   CU     0.03863  -0.02632   0.00000  -0.13359   0.09104   0.00000
   CU     2.43137   0.02632   0.00000   0.13359  -0.09104   0.00000
   S      1.23500   0.00000   1.87803   0.00000   0.00000  -0.28222
   S      1.23500   0.00000  -1.87803   0.00000   0.00000   0.28222
   N     -1.51240   1.26735   0.00000   0.11736  -0.09258   0.00000
   N      3.98240  -1.26735   0.00000  -0.11736   0.09258   0.00000
            6
   2 Ag, Cu-63                      obs.  260.00 cm-1, calc.  260.17 cm-1
   CU     0.01974  -0.01346   0.00000  -0.11471   0.07817   0.00000
   CU     2.45026   0.01346   0.00000   0.11471  -0.07817   0.00000
   S      1.23500   0.00000   1.83814   0.00000   0.00000  -0.24233
   S      1.23500   0.00000  -1.83814   0.00000   0.00000   0.24233
   N     -1.49582   1.25426   0.00000   0.10077  -0.07949   0.00000
   N      3.96582  -1.25426   0.00000  -0.10077   0.07949   0.00000
            6
   2 Ag, Cu-63                      obs.  260.00 cm-1, calc.  260.17 cm-1
   CU     0.00000   0.00000   0.00000  -0.09497   0.06472   0.00000
   CU     2.47000   0.00000   0.00000   0.09497  -0.06472   0.00000
   S      1.23500   0.00000   1.79643   0.00000   0.00000  -0.20062
   S      1.23500   0.00000  -1.79643   0.00000   0.00000   0.20062
   N     -1.47847   1.24058   0.00000   0.08343  -0.06581   0.00000
   N      3.94847  -1.24058   0.00000  -0.08343   0.06581   0.00000
            6
   2 Ag, Cu-63                      obs.  260.00 cm-1, calc.  260.17 cm-1
   CU    -0.01974   0.01346   0.00000  -0.07522   0.05126   0.00000
   CU     2.48974  -0.01346   0.00000   0.07522  -0.05126   0.00000
   S      1.23500   0.00000   1.75472   0.00000   0.00000  -0.15891
   S      1.23500   0.00000  -1.75472   0.00000   0.00000   0.15891
   N     -1.46112   1.22690   0.00000   0.06608  -0.05213   0.00000
   N      3.93112  -1.22690   0.00000  -0.06608   0.05213   0.00000
            6
   2 Ag, Cu-63                      obs.  260.00 cm-1, calc.  260.17 cm-1
   CU    -0.03863   0.02632   0.00000  -0.05634   0.03840   0.00000
   CU     2.50863  -0.02632   0.00000   0.05634  -0.03840   0.00000
   S      1.23500   0.00000   1.71483   0.00000   0.00000  -0.11902
   S      1.23500   0.00000  -1.71483   0.00000   0.00000   0.11902
   N     -1.44454   1.21381   0.00000   0.04949  -0.03904   0.00000
   N      3.91454  -1.21381   0.00000  -0.04949   0.03904   0.00000
            6
   2 Ag, Cu-63                      obs.  260.00 cm-1, calc.  260.17 cm-1
   CU    -0.05582   0.03804   0.00000  -0.03915   0.02668   0.00000
   CU     2.52582  -0.03804   0.00000   0.03915  -0.02668   0.00000
   S      1.23500   0.00000   1.67851   0.00000   0.00000  -0.08270
   S      1.23500   0.00000  -1.67851   0.00000   0.00000   0.08270
   N     -1.42943   1.20190   0.00000   0.03439  -0.02713   0.00000
   N      3.89943  -1.20190   0.00000  -0.03439   0.02713   0.00000
            6
   2 Ag, Cu-63                      obs.  260.00 cm-1, calc.  260.17 cm-1
   CU    -0.07057   0.04810   0.00000  -0.02439   0.01662   0.00000
   CU     2.54057  -0.04810   0.00000   0.02439  -0.01662   0.00000
   S      1.23500   0.00000   1.64734   0.00000   0.00000  -0.05153
   S      1.23500   0.00000  -1.64734   0.00000   0.00000   0.05153
   N     -1.41647   1.19167   0.00000   0.02143  -0.01690   0.00000
   N      3.88647  -1.19167   0.00000  -0.02143   0.01690   0.00000
            6
   2 Ag, Cu-63                      obs.  260.00 cm-1, calc.  260.17 cm-1
   CU    -0.08224   0.05605   0.00000  -0.01272   0.00867   0.00000
   CU     2.55224  -0.05605   0.00000   0.01272  -0.00867   0.00000
   S      1.23500   0.00000   1.62269   0.00000   0.00000  -0.02688
   S      1.23500   0.00000  -1.62269   0.00000   0.00000   0.02688
   N     -1.40622   1.18359   0.00000   0.01118  -0.00882   0.00000
   N      3.87622  -1.18359   0.00000  -0.01118   0.00882   0.00000
            6
   2 Ag, Cu-63                      obs.  260.00 cm-1, calc.  260.17 cm-1
   CU    -0.09032   0.06155   0.00000  -0.00465   0.00317   0.00000
   CU     2.56032  -0.06155   0.00000   0.00465  -0.00317   0.00000
   S      1.23500   0.00000   1.60563   0.00000   0.00000  -0.00982
   S      1.23500   0.00000  -1.60563   0.00000   0.00000   0.00982
   N     -1.39913   1.17799   0.00000   0.00408  -0.00322   0.00000
   N      3.86913  -1.17799   0.00000  -0.00408   0.00322   0.00000
            6
   2 Ag, Cu-63                      obs.  260.00 cm-1, calc.  260.17 cm-1
   CU    -0.09445   0.06436   0.00000  -0.00052   0.00035   0.00000
   CU     2.56445  -0.06436   0.00000   0.00052  -0.00035   0.00000
   S      1.23500   0.00000   1.59691   0.00000   0.00000  -0.00110
   S      1.23500   0.00000  -1.59691   0.00000   0.00000   0.00110
   N     -1.39550   1.17513   0.00000   0.00046  -0.00036   0.00000
   N      3.86550  -1.17513   0.00000  -0.00046   0.00036   0.00000
            6
   2 Ag, Cu-63                      obs.  260.00 cm-1, calc.  260.17 cm-1
   CU    -0.09445   0.06436   0.00000   0.18942  -0.12908   0.00000
   CU     2.56445  -0.06436   0.00000  -0.18942   0.12908   0.00000
   S      1.23500   0.00000   1.59691   0.00000   0.00000   0.40014
   S      1.23500   0.00000  -1.59691   0.00000   0.00000  -0.40014
   N     -1.39550   1.17513   0.00000  -0.16640   0.13126   0.00000
   N      3.86550  -1.17513   0.00000   0.16640  -0.13126   0.00000
            6
   2 Ag, Cu-63                      obs.  260.00 cm-1, calc.  260.17 cm-1
   CU    -0.09032   0.06155   0.00000   0.18529  -0.12627   0.00000
   CU     2.56032  -0.06155   0.00000  -0.18529   0.12627   0.00000
   S      1.23500   0.00000   1.60563   0.00000   0.00000   0.39142
   S      1.23500   0.00000  -1.60563   0.00000   0.00000  -0.39142
   N     -1.39913   1.17799   0.00000  -0.16277   0.12840   0.00000
   N      3.86913  -1.17799   0.00000   0.16277  -0.12840   0.00000
            6
   2 Ag, Cu-63                      obs.  260.00 cm-1, calc.  260.17 cm-1
   CU    -0.08224   0.05605   0.00000   0.17721  -0.12077   0.00000
   CU     2.55224  -0.05605   0.00000  -0.17721   0.12077   0.00000
   S      1.23500   0.00000   1.62269   0.00000   0.00000   0.37436
   S      1.23500   0.00000  -1.62269   0.00000   0.00000  -0.37436
   N     -1.40622   1.18359   0.00000  -0.15568   0.12280   0.00000
   N      3.87622  -1.18359   0.00000   0.15568  -0.12280   0.00000
            6
   2 Ag, Cu-63                      obs.  260.00 cm-1, calc.  260.17 cm-1
   CU    -0.07057   0.04810   0.00000   0.16554  -0.11281   0.00000
   CU     2.54057  -0.04810   0.00000  -0.16554   0.11281   0.00000
   S      1.23500   0.00000   1.64734   0.00000   0.00000   0.34971
   S      1.23500   0.00000  -1.64734   0.00000   0.00000  -0.34971
   N     -1.41647   1.19167   0.00000  -0.14543   0.11472   0.00000
   N      3.88647  -1.19167   0.00000   0.14543  -0.11472   0.00000
            6
   2 Ag, Cu-63                      obs.  260.00 cm-1, calc.  260.17 cm-1
   CU    -0.05582   0.03804   0.00000   0.15079  -0.10276   0.00000
   CU     2.52582  -0.03804   0.00000  -0.15079   0.10276   0.00000
   S      1.23500   0.00000   1.67851   0.00000   0.00000   0.31854
   S      1.23500   0.00000  -1.67851   0.00000   0.00000  -0.31854
   N     -1.42943   1.20190   0.00000  -0.13246   0.10449   0.00000
   N      3.89943  -1.20190   0.00000   0.13246  -0.10449   0.00000
            6
   2 Ag, Cu-63                      obs.  260.00 cm-1, calc.  260.17 cm-1
   CU    -0.03863   0.02632   0.00000   0.13359  -0.09104   0.00000
   CU     2.50863  -0.02632   0.00000  -0.13359   0.09104   0.00000
   S      1.23500   0.00000   1.71483   0.00000   0.00000   0.28222
   S      1.23500   0.00000  -1.71483   0.00000   0.00000  -0.28222
   N     -1.44454   1.21381   0.00000  -0.11736   0.09258   0.00000
   N      3.91454  -1.21381   0.00000   0.11736  -0.09258   0.00000
            6
   2 Ag, Cu-63                      obs.  260.00 cm-1, calc.  260.17 cm-1
   CU    -0.01974   0.01346   0.00000   0.11471  -0.07817   0.00000
   CU     2.48974  -0.01346   0.00000  -0.11471   0.07817   0.00000
   S      1.23500   0.00000   1.75472   0.00000   0.00000   0.24233
   S      1.23500   0.00000  -1.75472   0.00000   0.00000  -0.24233
   N     -1.46112   1.22690   0.00000  -0.10077   0.07949   0.00000
   N      3.93112  -1.22690   0.00000   0.10077  -0.07949   0.00000