Visualizing a computed structure - a commented example

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The Data

1. Obtain the data, the following structure was published in http://pubs.acs.org/cgi-bin/abstract.cgi/jacsat/2000/122/i37/abs/ja991878x.html

(Supporting Information)

45

Fe -0.055 0.033 -0.047 N -0.012 -1.496 1.451 N 0.015 -1.462 -1.372 N 0.000 1.386 1.481 N 0.070 1.417 -1.339 C -0.096 -1.304 2.825 C 0.028 -1.241 -2.739 C -0.066 -2.872 1.251 C -0.0159 -2.838 -1.205 C -0.064 1.164 2.850 C 0.070 1.226 -2.713 C 0.018 2.765 1.316 C 0.081 2.792 -1.142 C -0.175 -2.585 3.494 C 0.012 -2.508 -3.444 C -0.157 -3.550 2.526 C -0.015 -3.492 -2.498 C -0.077 2.431 3.552 C 0.093 2.507 -3.387 C -0.026 3.417 2.607 C 0.101 3.472 -2.420 H -0.245 -2.714 4.656 H 0.018 -2.611 -4.519 H -0.208 -4.622 2.648 H -0.035 -4.562 -2.644 H -0.125 2.535 4.626 H 0.099 2.635 -4.460 H -0.023 4.487 2.755 H 0.114 4.545 -2.543 C -0.108 -0.077 3.471 C 0.054 -0.001 -3.360 C 0.062 3.423 0.094 C -0.054 -3.499 0.014 H -0.168 -0.087 4.554 H 0.058 0.010 -4.445 H 0.069 4.508 0.106 H -0.092 -4.583 -0.002 O 2.045 -0.173 0.117 H 2.223 -0.959 0.670 S -2.348 -0.049 -0.003 H -2.554 1.318 -0.020 C 2.989 0.920 0.3529 H 2.709 1.705 0.345 H 4.006 0.577 0.139 H 2.913 1.290 1.378

2. Save the data to file.xyz

3. a) convert them to pdb with Openbabel (http://openbabel.org)

babel file.xyz file.pdb

or 3. b)

Open it with avogadro (http://avogadro.openmolecules.net) and save it as pdb. Avogadro allows you to adjust the coordinate sytem, which saves some work if you want to visualize several similar structures.

4. Save the following script to script.pml, open pymol and run the script with "@PATH_Of_The_Script/script.pml.