Client RMSF¶
Welcome to
_________ _______ _______ _______ _ _______ ______
\__ __/( ___ )|\ /|( ____ )( ____ \( ( /|( )( __ \
) ( | ( ) || ) ( || ( )|| ( \/| \ ( || () () || ( \ )
| | | (___) || | | || (____)|| (__ | \ | || || || || | ) |
| | | ___ || | | || __)| __) | (\ \) || |(_)| || | | |
| | | ( ) || | | || (\ ( | ( | | \ || | | || | ) |
| | | ) ( || (___) || ) \ \__| (____/\| ) \ || ) ( || (__/ )
)_( |/ \|(_______)|/ \__/(_______/|/ )_)|/ \|(______/
A command-line interface for Molecular Dynamics Analysis routines.
version: 0.11.2
Calculate RMSFS of a selection along the trajectory slice.¶
Algorithm¶
Calculates the RMSF values along a trajectory slice for different selections. If multiple selections are given creates a series data for that selection.
RMSF is calculated using libcalc.mda_rmsf.
If multiple selections are given, separate calculations are performed in sequence. Result files (data tables and plots) are exported separately for each selection. Selections can’t be overlayed easily in a single plot because they do not share the same labels.
Examples¶
Calculate RMSF of the whole system:
taurenmd rmsf top.pdb traj.dcd -e rmsf.csv
Calculates RMSFs for different selections:
taurenmd rmsf top.pdb traj.dcd -g 'segid A' 'segid B' -e
-x
exports the data to a CSV file. You can also plot the data with
the -v
option:
[...] -x rmsf.csv -v title=my-plot-title xlabel=frames ylabel=RMSFs ...
where [...]
is the previous command example.
you can also use tmdrmsf
instead of taurenmd rmsf
.
References¶
MD data accessed using MDAnalysis.
selection commands follow MDAnalysis selection nomenclature.
usage: tmdrmsf [-h] [-v] [-i] [-g SELECTIONS [SELECTIONS ...]]
[--inverted-selections INVERTED_SELECTIONS [INVERTED_SELECTIONS ...]]
[-s START] [-e STOP] [-p STEP] [-x [EXPORT]]
[--plot [PLOT [PLOT ...]]]
topology trajectories [trajectories ...]
Positional Arguments¶
- topology
Path to the topology file.
- trajectories
Path to the trajectory files. If multiple files are given, trajectories will be concatenated by input order.
Named Arguments¶
- -v, --version
show program’s version number and exit
- -i, --insort
Sorts input trajectories paths according to their tail numbers, if paths are formatted as follows: my_trajectory_#.dcd, where # is a number. Defaults to
False
.Default: False
- -g, --selections
List of atom selections to operate with. Selection rules are as defined by the MD analysis library used by the client interface. For instructions read the main command-line client description. Defaults to None, uses a single selection considering all atoms. Example: -g ‘segid A’ ‘segid B’ ‘name CA’
- --inverted-selections
Invert order of selections.
- -s, --start
The starting index for the frame slicing. Frames are 0-indexed, so the first frame is -s 0. The starting index is inclusive. Defaults to None, considers from the beginning.
- -e, --stop
The ending index for the frame slicing. Frames are 0-indexed, so the last frame of a 500 frame trajectory is index 499, but because the ending index is exclusive, -e 500 is required. Defaults to None, considers to the end.
- -p, --step
The periodicity step value for the frame slicing, -p 10 means every 10 frames. Defaults to None, considers every 1 frame.
- -x, --export
Export calculated values to a CSV file. Defaults to ‘results.csv’, alternatively, you can give a specific file name.
Default: False
- --plot
Plot results. Additional arguments can be given to configure the plot style. Example: –plot xlabel=frames ylabel=RMSD color=red.Accepted plot arguments are defined by the function used to plot the result. The main description of this client which plotting function is used. Defaults to
None
, no plot is produced.Default: False