Wiki source code of Distance-Fluctuations

Version 7.3 by emacasali on 2022/09/14 21:51

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5.1	5	= Distance Fluctuation (DF) Analysis =
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5.1	7	Giorgio Colombo Group (UNIPV)
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7.1	15	= What DF matrices are? =
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7.1	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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7.3	25	= How to use the script =
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7.3	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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