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 8.1
edited by emacasali
on 2022/09/14 21:52
Change comment: There is no comment for this version

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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 -
88 88  
89 89  )))
90 90  
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167 167  It is possible to obtain a distance fluctuation matrix average on protein domains ( or blocks).
168 168  
169 169  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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