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 ...)
 
(The Data)
Line 1: Line 1:
== 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
 
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)
+
in the Supporting Information
 
 
45
 
 
 
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
+
2. Save [[Media:File.xyz.tar|File.xyz.tar]] and untar it.
  
3. a) convert them to pdb with Openbabel (http://openbabel.org)
+
3. a) convert it to pdb with Openbabel (http://openbabel.org)
  
 
babel file.xyz file.pdb
 
babel file.xyz file.pdb
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Avogadro allows you to adjust the coordinate sytem, which saves some work if you want to visualize several similar structures.
 
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.
+
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.

Revision as of 19:04, 11 September 2008

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 in the Supporting Information

2. Save File.xyz.tar and untar it.

3. a) convert it 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 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.