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. Convert the file
    1. convert it to pdb with Openbabel
       babel file.xyz file.pdb
    2. Or: Open it with avogadro and save it as pdb. Avogadro allows you to adjust the coordinate system, which saves some work if you want to visualize several similar structures.
  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.
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