Summary

• Page properties (1 modified, 0 added, 0 removed)

Details

Page properties

Content

...	...	@@ -42,6 +42,50 @@
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	+
45	45	)))
46	46
47	47
...	...	@@ -57,4 +57,69 @@
57	57	)))
58	58	)))
59	59
60		-
	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.