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22	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 =
	25	+= Who has access? =
26	26
27		-• __Requisites__
28		-
29		- - Python 3.0 (or newer version)
30		-
31		- - Numpy
32		-
33		- - Scipy
34		-
35		-
36		-• __Usage__
37		-
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.
39		-
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).
41		-
42		-For more information run:
43		-
44		-{{{ python3 distance_fluctuation.py -h}}}
45		-
46		-
	27	+Describe the audience of this collab.
47	47	)))
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59	59	)))
60	60	)))
61		-
62		-• __How to read the output__
63		-
64		-The script generate different output file.
65		-
66		-
67		-A) Average Distance (avgdist) file:
68		-
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)
70		-
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).
72		-
73		- The distance is calculated as the average of the euclidean distance between the residues.
74		-
75		-
76		-B) Distance Fluctuation (rmsdist) file:
77		-
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).
79		-
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).
81		-
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:
83		-
84		- 1) Calculate the average euclidean distance between the residues (either CA or center of mass)
85		-
86		- 2) Calculate the average distance vector
87		-
88		- 3) Substract the distance fluctuation to the average distance
89		-
90		- 4) Calculate the power of the difference between distance fluctuation and local fluctuation
91		-
92		- 5) Filter the values of the close residues (1-x, x, 1+x)
93		-
94		- 6) Divide the obtained value for the number of frames
95		-
96		-
97		-C) Profile Sequence (profile_sequence) file:
98		-
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).
100		-
101		- The file is a vector containing the residue number and the local flucutation value.
102		-
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).
104		-
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).
106		-
107		-
108		-D) Distance Analysis (distance_analysis_out) file:
109		-
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).
111		-
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).
113		-
114		- The cutoff value is calculated as the sum between the nearcutoff and the tolerance value specified by the user.
115		-
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).
117		-
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)
119		-
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)
121		-
122		-
123		-E) Blocks Averaging: (rmsdist_out_b)
124		-
125		-It is possible to obtain a distance fluctuation matrix average on protein domains ( or blocks).
126		-
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.