Wiki source code of Distance-Fluctuations

Version 7.3 by emacasali on 2022/09/14 21:51
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5 = Distance Fluctuation (DF) Analysis =
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7 Giorgio Colombo Group (UNIPV)
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15 = What DF matrices are? =
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17 The analysis of the results of a MD simulation can performed using the Distance Fluctuation matrices (DF), based on the Coordination Propensity hypothesis:
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20 [[image:CodeCogsEqn-58.png||height="34" width="181"]]
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22 low CP values, corresponding to low pair-distance fluctuations, highlight groups of residues that move in a mechanically coordinated way.
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25 = How to use the script =
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27 • __Requisites__
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29 - Python 3.0 (or newer version)
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31 - Numpy
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33 - Scipy
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36 • __Usage__
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38 The script can analyze a MD trajectory and identify the coordinated motions between residues. It can then filter the output matrix based on the distance to identify long-range coordinated motions.
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40 The script can work both using only C-alphas (using either a pdb or a xyz file) or the sidechains (using a pdb file).
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42 For more information run:
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44 {{{ python3 distance_fluctuation.py -h}}}
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50 {{box title="**Contents**"}}
51 {{toc/}}
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54 {{/box}}
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