Team:TU-Munich/Results/How To

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Revision as of 20:52, 28 September 2013 by AndiB (Talk | contribs)


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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