Difference between revisions of "Visualizing a computed structure - a commented example"

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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
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# Obtain the [http://pubs.acs.org/cgi-bin/abstract.cgi/jacsat/2000/122/i37/abs/ja991878x.html data], the following structure was published in [http://pubs.acs.org/journals/jacsat/index.html J. Am. Chem. Soc.] in the Supporting Information
in the Supporting Information
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# Save [[Media:File.xyz.tar|File.xyz.tar]] and untar it.
 
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# Convert the file
2. Save [[Media:File.xyz.tar|File.xyz.tar]] and untar it.
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## convert it to pdb with [http://openbabel.org Openbabel] <source lang="python"> babel file.xyz file.pdb</source>
 
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## 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.
3. a) convert it to pdb with Openbabel (http://openbabel.org)
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# 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-File. Open pymol and run the script with "@PATH_Of_The_Script/script.pml".
 
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# You will get the following image, you can save it with "png filename.png" [[Image:File.png]]
babel file.xyz file.pdb
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# Use the script to modify your own pdb-file.
 
 
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 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-File. Open pymol and run the script with "@PATH_Of_The_Script/script.pml.
 
 
 
5. You will get the following image, you can save it with "png filename.png"
 
 
 
[[Image:File.png]]
 
 
 
6. 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 09:01, 12 September 2008

  1. Obtain the data, the following structure was published in J. Am. Chem. Soc. in the Supporting Information
  2. Save File.xyz.tar and untar it.
  3. Convert the file
    1. convert it to pdb with Openbabel
       babel file.xyz file.pdb
      
    2. 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.
  4. 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-File. Open pymol and run the script with "@PATH_Of_The_Script/script.pml".
  5. You will get the following image, you can save it with "png filename.png" File.png
  6. Use the script to modify your own pdb-file.