Difference between revisions of "Visualizing a computed structure - a commented example"
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Qqqqqqqqq9 (talk | contribs) (The supporting Information contains several structures. Unfortunatly the pdf is a pixel-PDF, i typewrote them and save them to File.xyz.tar) |
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− | # Obtain the [ | + | # Obtain the [[Media:File.xyz.tar|File.xyz.tar]] and untar it. It contains the coordinates, which were originally published in [http://pubs.acs.org/journals/jacsat/index.html J. Am. Chem. Soc.] in the Supporting Information of this [http://pubs.acs.org/cgi-bin/abstract.cgi/jacsat/2000/122/i37/abs/ja991878x.html article]. |
− | |||
# Convert the file | # Convert the file | ||
## convert it to pdb with [http://openbabel.org Openbabel] <source lang="python"> babel file.xyz file.pdb</source> | ## convert it to pdb with [http://openbabel.org Openbabel] <source lang="python"> babel file.xyz file.pdb</source> | ||
− | ## Open it with [http://avogadro.openmolecules.net 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. | + | ## Or: Open it with [http://avogadro.openmolecules.net 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. |
− | # Save the following pymolscript [[Media:script.pml.tar|Script.pml.tar]] and untar it to script.pml. Open it with an editor and adjust the Path_To_The_PDB | + | # Save the following pymolscript [[Media:script.pml.tar|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". |
# You will get the following image, you can save it with "png filename.png" [[Image:File.png]] | # You will get the following image, you can save it with "png filename.png" [[Image:File.png]] | ||
# Use the script to modify your own pdb-file. | # Use the script to modify your own pdb-file. | ||
[[Category:Tutorials|Visualizing a computed structure - a commented example]] | [[Category:Tutorials|Visualizing a computed structure - a commented example]] |
Revision as of 11:03, 14 September 2008
- 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.
- Convert the file
- 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".
- You will get the following image, you can save it with "png filename.png"
- Use the script to modify your own pdb-file.