Team:TU-Munich/Results/How To

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==Generation of Annimated GIFs showing PDB files in 3D==
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*A homology search was performed for the amino acid sequece using [http://toolkit.tuebingen.mpg.de/hhpred HHpred]
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*Entry for the best matching structure(> 50%)in PDB-database was opened
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*PDB-file was  was saved
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*The structure was opened with Pymol
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*The approach was adapted from a PyMol-Tutorial [[http://ihome.cuhk.edu.hk/~b102142/pymol/pymol_tutorial.html Wong]]
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*The following commands were entered into the command line:
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<code>
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PyMOL> orient<br>
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PyMOL> hide everything, all<br>
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PyMOL> show cartoon, all<br>
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PyMol> bg_color white<br>
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click> Settings>Rendering>Shadows>Occlusion<br>
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PyMOL> color purple, ss h; color yellow, ss s; color green, ss ""<br>
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PyMOL> show surface, all<br>
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PyMOL> set transparency, 0.75<br>
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PyMOL> set surface_quality, 1    (command will prolongue the process significantly, you may skip it)<br>
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PyMOL> set ray_trace_frames=1    (command will prolongue the process significantly, you may skip it)<br>
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PyMOL> mset 1 x180<br>
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PyMOL> util.mroll 1,180<br>
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PyMOL> mpng frame<br>
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</code>
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*Afterward the *.png files were automatically converted to *.tif files using xxx
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*The program xxx was used to generate the annimated GIFs
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**A new working folder was generated and the *.gif files were imported
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**The background was set to white
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**The range of colors was set to 256
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**Finally the annimated Gif was computed
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The result is the following:<br>
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[[File:TUM13_Annimated_Gif_test.gif|thumb|left|320px|Description]]
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Revision as of 20:52, 28 September 2013


Generation of Annimated GIFs showing PDB files in 3D

  • A homology search was performed for the amino acid sequece using [http://toolkit.tuebingen.mpg.de/hhpred HHpred]
  • Entry for the best matching structure(> 50%)in PDB-database was opened
  • PDB-file was was saved
  • The structure was opened with Pymol
  • The approach was adapted from a PyMol-Tutorial http://ihome.cuhk.edu.hk/~b102142/pymol/pymol_tutorial.html Wong
  • The following commands were entered into the command line:

PyMOL> orient
PyMOL> hide everything, all
PyMOL> show cartoon, all
PyMol> bg_color white
click> Settings>Rendering>Shadows>Occlusion
PyMOL> color purple, ss h; color yellow, ss s; color green, ss ""
PyMOL> show surface, all
PyMOL> set transparency, 0.75
PyMOL> set surface_quality, 1 (command will prolongue the process significantly, you may skip it)
PyMOL> set ray_trace_frames=1 (command will prolongue the process significantly, you may skip it)
PyMOL> mset 1 x180
PyMOL> util.mroll 1,180
PyMOL> mpng frame

  • Afterward the *.png files were automatically converted to *.tif files using xxx
  • The program xxx was used to generate the annimated GIFs
    • A new working folder was generated and the *.gif files were imported
    • The background was set to white
    • The range of colors was set to 256
    • Finally the annimated Gif was computed

The result is the following:

File:TUM13 Annimated Gif test.gif
Description

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