Visualizing a computed structure - a commented example

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Revision as of 11:03, 14 September 2008 by Qqqqqqqqq9 (talk | contribs) (The supporting Information contains several structures. Unfortunatly the pdf is a pixel-PDF, i typewrote them and save them to
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  1. Obtain the 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.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.