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42	42	For more information run:
43	43
44	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		-
89	89	)))
90	90
91	91
...	...	@@ -101,69 +101,4 @@
101	101	)))
102	102	)))
103	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.
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