Difference between revisions of "MD simulation analysis TSD Journal"
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| + | Back to [[MD simulation analysis TSD|results]]. |
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| − | Journal for |
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| − | == alice == |
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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. |
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| + | |||
| + | =Ramachandran plots= |
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| + | At first the .xvg files were parsed into the following format: |
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| + | ID Psi Phi Aa |
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| + | 1HMP:chain0:Pro5 -92.926842 12.941312 Proline |
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| + | 1HMP:chain0:Gly6 65.796807 -162.229709 Glycine |
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| + | 1HMP:chain0:Val7 -81.132082 121.413022 General |
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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> |
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| + | 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]. |
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| + | |||
| + | =Significance calculation= |
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| + | The p-value was computed with the script statTD.pl. |
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Latest revision as of 20:39, 31 August 2012
Back to results.
Contents
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.
