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Changes for page Distance-Fluctuations

Last modified by emacasali on 2022/09/15 13:34
From version 8.1
edited by emacasali
on 2022/09/14 21:52
Change comment: There is no comment for this version
To version 6.1
edited by emacasali
on 2022/09/14 21:41
Change comment: Uploaded new attachment "CodeCogsEqn-58.png", version {1}

Summary

Details

Page properties
Content
... ... @@ -12,38 +12,15 @@
12 12  (((
13 13  (% class="col-xs-12 col-sm-8" %)
14 14  (((
15 -= What DF matrices are? =
15 += What can I find here? =
16 16  
17 -The analysis of the results of a MD simulation can performed using the Distance Fluctuation matrices (DF), based on the Coordination Propensity hypothesis:
17 +* Notice how the table of contents on the right
18 +* is automatically updated
19 +* to hold this page's headers
18 18  
19 -(% style="text-align:center" %)
20 -[[image:CodeCogsEqn-58.png||height="34" width="181"]]
21 += Who has access? =
21 21  
22 -low CP values, corresponding to low pair-distance fluctuations, highlight groups of residues that move in a mechanically coordinated way.
23 -
24 -
25 -= How to use the script =
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 -
23 +Describe the audience of this collab.
47 47  )))
48 48  
49 49  
... ... @@ -51,77 +51,8 @@
51 51  (((
52 52  {{box title="**Contents**"}}
53 53  {{toc/}}
54 -
55 -
56 56  {{/box}}
57 57  
58 58  
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.