PyMOL Wiki - User contributions [en]

Visualizing a computed structure - a commented example

2008-09-14T15:03:59Z

Qqqqqqqqq9: The supporting Information contains several structures. Unfortunatly the pdf is a pixel-PDF, i typewrote them and save them to File.xyz.tar

# 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].
# Convert the file
## convert it to pdb with [http://openbabel.org Openbabel] <source lang="python"> babel file.xyz file.pdb</source>
## 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. 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]]
# Use the script to modify your own pdb-file.
[[Category:Tutorials|Visualizing a computed structure - a commented example]]

Visualizing a computed structure - a commented example

2008-09-12T11:35:30Z

Qqqqqqqqq9:

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 [[Media:File.xyz.tar|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 [[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]]

Visualizing a computed structure - a commented example

2008-09-11T23:04:32Z

Qqqqqqqqq9: /* The Data */

File:File.png

2008-09-11T23:00:53Z

Qqqqqqqqq9:

File:Script.pml.tar

2008-09-11T23:00:35Z

Qqqqqqqqq9: uploaded a new version of "Image:Script.pml.tar": Pymol-Script

File:Script.pml.tar

2008-09-11T23:00:07Z

Qqqqqqqqq9:

File:File.xyz.tar

2008-09-11T22:21:36Z

Qqqqqqqqq9: xyz-coordinatinates of the Produkt in the Dublett-states obtained from http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ja991878x

xyz-coordinatinates of the Produkt in the Dublett-states obtained from

http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ja991878x

Visualizing a computed structure - a commented example

2008-09-11T22:17:02Z

Qqqqqqqqq9: 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 ==

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

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.