A tool to calculate FRET observables for MD trajectories by accessible volume calculations.Here, spatial density of flexible coupled dyes/labels is approximated by the sterically allowedspace for labels modeled by ellipsoids attached by a flexible cylinder.
MDTrajFPS is tool to calculate FRET observables from MD-trajectories.
MDTrajFPS depends on MDTraj and utilizes the original libraries published together with the "FRET Positioning System" (FPS) in Nature Methods 9, 1218–1225 (2012) "A toolkit and benchmark study for FRET-restrained high-precision structural modeling".
The implicit model of the label is being improved to support the latest developments . Hence, the library for the calculation of the implicit labels are currently only provided as pre-compiled binaries for (Windows x32, x64, MacOS, and Linux x32, x64).
With MDTrajFPS, you can
- Process every MD format supported by MDTraj
- Calculate FRET efficienes using a fast implicit dye model
- Save calculated positional distributions of dyes for later vizualization
The original FPS-software package is available at http://www.mpc.hhu.de/software/fps.html.
conda --add channels tpeulen conda install mdtraj_fps
import mdtraj as md from mdtraj_fps import fps # First load an MD trajectory by mdtraj traj = md.load('./examples/hGBP1_out_3.h5') # Pass a trajectory to fps.AVTrajectory. This creates an object, which can be # accessed as a list. The objects within the "list" are accessible volumes av_traj = fps.AVTrajectory(traj, '18D', attachment_atom_selection='resSeq 7 and name CB') # These accessible volumes can be saved as xyz-file av_traj.save_xyz('test_344.xyz') # The dye parameters can either be passed explicitly on creation of the object av_traj = fps.AVTrajectory(traj, '18D', attachment_atom_selection='resSeq 7 and name CB', linker_length=25., linker_width=1.5, radius_1=6.0) # or they can be selected from a predefined set of parameters found in the JSON file dye_definition.json located within # the package directory av_traj = fps.AVTrajectory(traj, '18D', attachment_atom_selection='resSeq 7 and name CB', dye_parameter_set='D3Alexa488') # To calculate a trajectory of distances and distance distributions first a labeling file and a "distance file" # needs to be specified. The distance file contains a set of labeling positions and distances and should be compatible # to the labeling files used by the software "Olga". By default the av_dist = fps.AvDistanceTrajectory(traj, './examples/hGBP1_distance.json')
The windows dll requires the following redistributables (not included)
MS-visual studio 2005 vcredist_x64 vcredist_x86
GNU LGPL version 2.1, or at your option a later version of the license. Various sub-portions of this library may be independently distributed under different licenses. See those files for their specific terms.