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

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(PyMOl can open xyz files)
 
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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
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# 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].
# Save [[Media:File.xyz.tar|File.xyz.tar]] and untar it.
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# Open the file with PyMOL and save it as a pdb file.
# Convert the file
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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. Open pymol and run the script with "@PATH_Of_The_Script/script.pml".
## 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.
 
# 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".
 
 
# 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]]

Latest revision as of 03:35, 21 October 2015

  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.