Visualizing a computed structure - a commented example

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  1. Obtain the File.xyz.tar and untar it. It contains the coordinates, which were originally published in J. Am. Chem. Soc. in the Supporting Information of this article.
  2. Open the file with PyMOL and save it as a pdb file.
  3. Save the following pymolscript Script.pml.tar and untar it to script.pml. Open it with an editor and adjust the Path_To_The_PDB. Open pymol and run the script with "@PATH_Of_The_Script/script.pml".
  4. You will get the following image, you can save it with "png filename.png" File.png
  5. Use the script to modify your own pdb-file.