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

From PyMOLWiki
Jump to: navigation, search
(The supporting Information contains several structures. Unfortunatly the pdf is a pixel-PDF, i typewrote them and save them to File.xyz.tar)
Line 1: Line 1:
# 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
+
# 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.
 
 
# 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-File. Open pymol and run the script with "@PATH_Of_The_Script/script.pml".
+
# 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

  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.