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Changes for page Distance-Fluctuations

Last modified by emacasali on 2022/09/15 13:34
From version 14.1
edited by emacasali
on 2022/09/15 13:34
Change comment: There is no comment for this version
To version 7.1
edited by emacasali
on 2022/09/14 21:47
Change comment: There is no comment for this version

Summary

Details

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Content
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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.
23 23  
24 24  
25 -= How to use the script =
25 +== Who has access? ==
26 26  
27 -• __Requisites__
27 +Describe the audience of this collab.
28 28  
29 - - Python 3.0 (or newer version)
30 30  
31 - - Numpy
30 += Who has access? =
32 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 -
47 -{{{optional arguments:
48 - -h, --help show this help message and exit
49 -
50 -Required arguments:
51 - -ext {pdb,xyz}, --file_ext {pdb,xyz}
52 - Input trajectory file iformat (options: .pdb or .xyz)
53 - -n N_AA, --n_aa N_AA Number of aminoacids in each frame of the .pdb
54 - trajectory
55 -
56 -Optional arguments:
57 - -i IN_NAME, --in_name IN_NAME
58 - Name of the trajectory file (default: trj)
59 - -s S_FRAME, --s_frame S_FRAME
60 - Index of the initial frame (default = 0)
61 - -e E_FRAME, --e_frame E_FRAME
62 - Index of the last frame (default = end)
63 - -c CUTOFF, --cutoff CUTOFF
64 - Cutoff for the distance fluctuation analysis (default = 5)
65 - -t TOLERANCE, --tolerance TOLERANCE
66 - Tolerance for the distance fluctuation analysis (default = 0)
67 - -p {all,c-a}, --pdb_type {all,c-a}
68 - Type of pdb file submitted (only C-alpha, all protein atoms)
69 - -l {s,seq,v,volume}, --local {s,seq,v,volume}
70 - Type of local cutoff used, sequence or volume (default = seq)
71 - -r RADIUS, --radius RADIUS
72 - Radius of the area cutoff (default = 7A)
73 - -rs RES_START, --res_start RES_START
74 - Starting residue if the PDB does not start with res.num. 1
75 - -ro RMS_OUT, --rms_out RMS_OUT
76 - RMS distance output filename (without extension)
77 - -ao AVG_OUT, --avg_out AVG_OUT
78 - Average distance output filename (without extension)
79 - -so SEQ_OUT, --seq_out SEQ_OUT
80 - Profile sequence output filename (without extension)
81 - -da DIST_AN, --dist_an DIST_AN
82 - Distance analysis output filename (without extension)
83 - --blocks BLOCKS File with domains borders
84 -
85 - -rb RMS_B_OUT, --rms_b_out RMS_B_OUT
86 - RMS distance blocks output filename}}}
87 -
88 -
32 +Describe the audience of this collab.
89 89  )))
90 90  
91 91  
... ... @@ -100,75 +100,3 @@
100 100  
101 101  )))
102 102  )))
103 -
104 -• __How to read the output__
105 -
106 -The script generate different output file.
107 -
108 -
109 -A) Average Distance (avgdist) file:
110 -
111 - 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)
112 -
113 - 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).
114 -
115 - The distance is calculated as the average of the euclidean distance between the residues.
116 -
117 -
118 -B) Distance Fluctuation (rmsdist) file:
119 -
120 - 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).
121 -
122 - The file contains a matrix using the residue indexes as axes and the distance fluctuation between the residues as the data (r1 r2 rmsdist).
123 -
124 - 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:
125 -
126 - 1) Calculate the average euclidean distance between the residues (either CA or center of mass)
127 -
128 - 2) Calculate the average distance vector
129 -
130 - 3) Substract the distance fluctuation to the average distance
131 -
132 - 4) Calculate the power of the difference between distance fluctuation and local fluctuation
133 -
134 - 5) Filter the values of the close residues (1-x, x, 1+x)
135 -
136 - 6) Divide the obtained value for the number of frames
137 -
138 -
139 -C) Profile Sequence (profile_sequence) file:
140 -
141 - 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).
142 -
143 - The file is a vector containing the residue number and the local flucutation value.
144 -
145 - 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).
146 -
147 - 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).
148 -
149 -
150 -D) Distance Analysis (distance_analysis_out) file:
151 -
152 - 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).
153 -
154 - 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).
155 -
156 - The cutoff value is calculated as the sum between the nearcutoff and the tolerance value specified by the user.
157 -
158 - 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).
159 -
160 - 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)
161 -
162 - 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)
163 -
164 -
165 -E) Blocks Averaging: (rmsdist_out_b)
166 -
167 -It is possible to obtain a distance fluctuation matrix average on protein domains ( or blocks).
168 -
169 -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.
170 -
171 -
172 -= References =
173 -
174 -Morra, G.; Potestio, R.; Micheletti, C.; Colombo, G., Corresponding Functional Dynamics across the Hsp90 Chaperone Family: Insights from a Multiscale Analysis of MD Simulations, PLOS Computational Biology 8(3): e1002433. [[https:~~/~~/doi.org/10.1371/journal.pcbi.1002433>>url:https://doi.org/10.1371/journal.pcbi.1002433]]
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