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Wiki source code of Distance-Fluctuations

Version 8.1 by emacasali on 2022/09/14 21:52
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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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52 {{box title="**Contents**"}}
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62 • __How to read the output__
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64 The script generate different output file.
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67 A) Average Distance (avgdist) file:
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69 The name of the file is avgdist_out_x_y_type.dat with x = start frame of the analysis, y = end frame of the analysis, type = type of analysis (CA or sidechains)
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71 The file contains a matrix using the residue indexes as axes and the average value of the distance between the residues as the data (r1 r2  avgdist).
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73 The distance is calculated as the average of the euclidean distance between the residues.
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76 B) Distance Fluctuation (rmsdist) file:
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78 The name of the file is rmsdist_out_x_y_type.dat with x = start frame of the analysis, y = end frame of the analysis, type = type of analysis (CA or sidechains).
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80 The file contains a matrix using the residue indexes as axes and the distance fluctuation between the residues as the data (r1 r2 rmsdist).
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82 The distance fluctuation is calculated for the residues that are at least 3 residues away from each other (x-2 to x+2) as follow:
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84 1) Calculate the average euclidean distance between the residues (either CA or center of mass)
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86 2) Calculate the average distance vector
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88 3) Substract the distance fluctuation to the average distance
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90 4) Calculate the power of the difference between distance fluctuation and local fluctuation
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92 5) Filter the values of the close residues (1-x, x, 1+x)
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94 6) Divide the obtained value for the number of frames
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97 C) Profile Sequence (profile_sequence) file:
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99 The name of the file is profile_sequence_x_y_type.dat with x = start frame of the analysis, y = end frame of the analysis, type = type of analysis (CA or sidechains).
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101 The file is a vector containing the residue number and the local flucutation value.
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103 The local fluctuation is calculated as the average fluctuation of the residues close to each other (that is the residues ranging from x-2 to x+2 with x = residue number).
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105 Since the value contains the average distance fluctuation for a range of residues the output starts from residue 4 and ends at residue n-3).
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108 D) Distance Analysis (distance_analysis_out) file:
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110 The name of the file is distance_analysis_out_c_x_y_type.dat with c = cutoff value, x = start frame of the analysis, y = end frame of the analysis, type = type of analysis (CA or sidechains).
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112 This fail contains the distance fluctuation filtered by the cutoff value (the value are kept if the distance fluctuation is smaller than the cutoff value).
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114 The cutoff value is calculated as the sum between the nearcutoff and the tolerance value specified by the user.
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116 The nearcutoff can be calcolated either using sequence proximity or 3d proximity and can be specified by command line using the option -l or ~-~-local (see the command line help for further details).
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118 In the case of sequence proximity it is calculated as the average of the distance fluctuation value for residues in the range of x-2,x+2 (x = residue index)
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120 In the case of 3d proximity is calculated as the average distance fluctuation of the residues within a certain radius from the current one (default value = 6.5 A)
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123 E) Blocks Averaging: (rmsdist_out_b)
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125 It is possible to obtain a distance fluctuation matrix average on protein domains ( or blocks).
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127 The script requires an input file with the borders of the protein blocks defined by the user, in the form of two columns: the first with the lower limit and the second with the upper limit.