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

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(New page: == The Data == 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 (Supporting Information) 45 ...)
 
(PyMOl can open xyz files)
 
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== The Data ==
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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].
 
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# Open the file with PyMOL and save it as a pdb file.
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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# 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".
(Supporting Information)
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# You will get the following image, you can save it with "png filename.png" [[Image:File.png]]
 
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# Use the script to modify your own pdb-file.
45
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[[Category:Tutorials|Visualizing a computed structure - a commented example]]
 
 
Fe -0.055 0.033 -0.047
 
N -0.012 -1.496 1.451
 
N 0.015 -1.462 -1.372
 
N 0.000 1.386 1.481
 
N 0.070 1.417 -1.339
 
C -0.096 -1.304 2.825
 
C 0.028 -1.241 -2.739
 
C -0.066 -2.872 1.251
 
C -0.0159 -2.838 -1.205
 
C -0.064 1.164 2.850
 
C 0.070 1.226 -2.713
 
C 0.018 2.765 1.316
 
C 0.081 2.792 -1.142
 
C -0.175 -2.585 3.494
 
C 0.012 -2.508 -3.444
 
C -0.157 -3.550 2.526
 
C -0.015 -3.492 -2.498
 
C -0.077 2.431 3.552
 
C 0.093 2.507 -3.387
 
C -0.026 3.417 2.607
 
C 0.101 3.472 -2.420
 
H -0.245 -2.714 4.656
 
H 0.018 -2.611 -4.519
 
H -0.208 -4.622 2.648
 
H -0.035 -4.562 -2.644
 
H -0.125 2.535 4.626
 
H 0.099 2.635 -4.460
 
H -0.023 4.487 2.755
 
H 0.114 4.545 -2.543
 
C -0.108 -0.077 3.471
 
C 0.054 -0.001 -3.360
 
C 0.062 3.423 0.094
 
C -0.054 -3.499 0.014
 
H -0.168 -0.087 4.554
 
H 0.058 0.010 -4.445
 
H 0.069 4.508 0.106
 
H -0.092 -4.583 -0.002
 
O 2.045 -0.173 0.117
 
H 2.223 -0.959 0.670
 
S -2.348 -0.049 -0.003
 
H -2.554 1.318 -0.020
 
C 2.989 0.920 0.3529
 
H 2.709 1.705 0.345
 
H 4.006 0.577 0.139
 
H 2.913 1.290 1.378
 
 
 
2. Save the data to file.xyz
 
 
 
3. a) convert them to pdb with Openbabel (http://openbabel.org)
 
 
 
babel file.xyz file.pdb
 
 
 
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 script to script.pml, open pymol and run the script with "@PATH_Of_The_Script/script.pml.
 

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.