Difference between revisions of "MD simulation analysis TSD Journal"

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(Signifikance calculation)
 
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Back to [[MD simulation analysis TSD|results]].
 
Back to [[MD simulation analysis TSD|results]].
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=General=
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Most of the base data was calculated according to the tutorial with a slightly modified version of scripts by Hemochromatosis. These are [https://gist.github.com/3557972 calcData.pl], [https://gist.github.com/3557978 create.sh], [https://gist.github.com/3557985 xmgrace.sh] for creating the plots and [https://gist.github.com/3557996 convert.sh] to convert the plots to PNG.
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=Trajectories=
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PNGs were created with [https://gist.github.com/3557863 createTrajectories.pml] and then combined into an animation with [https://gist.github.com/3557814 createAnim.sh].
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=Thermodynamics=
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Averages were calculated with R's "summary" function on grep-truncated xvg files.
   
 
=Ramachandran plots=
 
=Ramachandran plots=
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1HMP:chain0:Val7 -81.132082 121.413022 General
 
1HMP:chain0:Val7 -81.132082 121.413022 General
   
Additionally the data for the background distribution was loaded from [http://www2.warwick.ac.uk/fac/sci/moac/people/students/peter_cock/r/ramachandran/#downloads|here].<br>
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Additionally the data for the background distribution was downloaded from [http://www2.warwick.ac.uk/fac/sci/moac/people/students/peter_cock/r/ramachandran/#downloads|here].<br>
 
Then the scipt [https://gist.github.com/3557539|draw_rama.R] was called.
 
Then the scipt [https://gist.github.com/3557539|draw_rama.R] was called.
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=B-Factor=
 
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Plots for comparing B-Factor based on all atoms and only C-alpha atoms were created with [https://gist.github.com/3557912 plotBFactors.pml].
   
 
=Significance calculation=
 
=Significance calculation=

Latest revision as of 20:39, 31 August 2012

Back to results.

General

Most of the base data was calculated according to the tutorial with a slightly modified version of scripts by Hemochromatosis. These are calcData.pl, create.sh, xmgrace.sh for creating the plots and convert.sh to convert the plots to PNG.

Trajectories

PNGs were created with createTrajectories.pml and then combined into an animation with createAnim.sh.

Thermodynamics

Averages were calculated with R's "summary" function on grep-truncated xvg files.

Ramachandran plots

At first the .xvg files were parsed into the following format:

ID                       Psi              Phi             Aa
1HMP:chain0:Pro5	-92.926842	12.941312	Proline
1HMP:chain0:Gly6	65.796807	-162.229709	Glycine
1HMP:chain0:Val7	-81.132082	121.413022	General

Additionally the data for the background distribution was downloaded from [1].
Then the scipt [2] was called.

B-Factor

Plots for comparing B-Factor based on all atoms and only C-alpha atoms were created with plotBFactors.pml.

Significance calculation

The p-value was computed with the script statTD.pl.