Team:TU-Munich/Results/How To

From 2013.igem.org

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**The range of colors was set to 256 (Edit>Select_all and Edit>Change_Color)
**The range of colors was set to 256 (Edit>Select_all and Edit>Change_Color)
**The size of the file has to be reduced in order to be able to upload it on the iGEM wiki. This can be done by clicking Edit>Change_size. We suggest a size of 320x240 px or even samler if the resulting Gif becomes to big.
**The size of the file has to be reduced in order to be able to upload it on the iGEM wiki. This can be done by clicking Edit>Change_size. We suggest a size of 320x240 px or even samler if the resulting Gif becomes to big.
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**Finally the annimated Gif can be saved in the programm format (.xxx) and as Gif (File>Save_as)
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**Finally the annimated Gif can be saved in the programm format (.abp) and as Gif (File>Save_as)
**If you have problems to upload the file on the iGEM server you may try a reduced size (e.g. 300x225 px)
**If you have problems to upload the file on the iGEM server you may try a reduced size (e.g. 300x225 px)
This is how your protein of interest could look like:<br>
This is how your protein of interest could look like:<br>
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[[File:TUM13_Annimated_test.gif|thumb|left|320px|Description]]
+
[[File:TUM13_Annimated_test.gif|thumb|right|320px|Description]]
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Revision as of 22:01, 28 September 2013


Our How To Tutorials

During our iGEM summer we have learned some skills which are useful for iGEM and also for any synthetic biologist. In order to conservate and spread this knowledge we created some How To Tutorials. We hope that these Tutorials help iGEM teams in the future to present their project in a more colorful fashion.


Generation of Annimated Gifs showing PDB files in 3D

The generation of animated Gif from PDB files was done sice some time in the iGEM competition. Here we present an easy to reproduce tutorial for iGEMers which are interested in such figures.

  • If there is no PDB file availible for your protein of interest, you may use a homology search to find the most homologue structure. For this homology search you have to enter the amino acid sequece for example into [http://toolkit.tuebingen.mpg.de/hhpred HHpred]
  • The entry for the best matching structure was used for the figure. If it is only a homologous structure please cite this together with the homology when presenting the resulting Gif.
  • You can save the PDB file of the homologous structure on your computer
  • If you do not have [http://www.pymol.org/ PyMol] (freeware) installed on your computer download and install it.
  • Start PyMol software and open the PDB-file by clicking File>Open
  • The following 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 [http://www.xnview.com/de/xnconvert/ XnConvert]
  • The program [http://www.animake.de/gif-animation.htm Animake] was used to generate the annimated GIFs
    • The Animake software was started
    • A new working folder was generated (File>New) and the *.gif files were imported (Edit>Import_from_file)
    • The background was set to white (Annimation>Settings)
    • The range of colors was set to 256 (Edit>Select_all and Edit>Change_Color)
    • The size of the file has to be reduced in order to be able to upload it on the iGEM wiki. This can be done by clicking Edit>Change_size. We suggest a size of 320x240 px or even samler if the resulting Gif becomes to big.
    • Finally the annimated Gif can be saved in the programm format (.abp) and as Gif (File>Save_as)
    • If you have problems to upload the file on the iGEM server you may try a reduced size (e.g. 300x225 px)

This is how your protein of interest could look like:

File:TUM13 Annimated test.gif
Description

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