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...	...	@@ -43,6 +43,48 @@
43	43
44	44	{{{ python3 distance_fluctuation.py -h}}}
45	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	+
46	46
47	47	)))
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...	...	@@ -125,3 +125,8 @@
125	125	It is possible to obtain a distance fluctuation matrix average on protein domains ( or blocks).
126	126
127	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.
	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]]