Warning: The EBRAINS Drive and EBRAINS Lab will down on Tuesday, the 8th of July 2025 starting from 5pm CEST (my timezone) for up to 1 hour.


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 12.1
edited by emacasali
on 2022/09/15 13:34
Change comment: There is no comment for this version

Summary

Details

Page properties
Content
... ... @@ -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  )))
48 48  
... ... @@ -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]]
XWiki.XWikiRights[3]
Allow/Deny
... ... @@ -1,0 +1,1 @@
1 +Allow
Levels
... ... @@ -1,0 +1,1 @@
1 +view
Users
... ... @@ -1,0 +1,1 @@
1 +XWiki.XWikiGuest