NAFlex Standard Cartesian Analysis
NAFlex implements a set of Standard Cartesian Analysis taken directly from our MDWeb server. The most important ones are listed below.
Apart from these ones, operations to transform between trajectory formats, extract snapshots or slices from trajectories, tools to compress/uncompress trajectories (pcazip tool) are also implemented. More information about all of these operations can be found in MDWeb help pages (MDWeb Operations).
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Plot RMSd along the trajectory
Root Mean Square deviation along the trajectory.
Programs: Ptraj from AmberTools package (Binpos,Crd,DCD,NetCDF trajectory formats). g_rms from Gromacs package (XTC trajectory format).
- Possibility to select a subset of atoms/residues from the whole system.
- User defined Mask only available for ptraj-compatible trajectory formats (Binpos,Crd,DCD,NetCDF).
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Plot RMSd x Residue
Average Root Mean Square deviation per residue along the trajectory.
Programs: Ptraj from AmberTools package (Binpos,Crd,DCD,NetCDF trajectory formats). g_rmsf from Gromacs package (XTC trajectory format).
- Possibility of use a reference structure (PDB format).
- Possibility to select a subset of atoms/residues from the whole system.
- User defined Mask only available for ptraj-compatible trajectory formats (Binpos,Crd,DCD,NetCDF).
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Plot BFactor per residue
Gets Bfactor values per residue from a Trajectory.
Programs: Ptraj from AmberTools package (Binpos,Crd,DCD,NetCDF trajectory formats). g_rmsf from Gromacs package (XTC trajectory format).
- Possibility to select a subset of atoms/residues from the whole system.
- User defined Mask only available for ptraj-compatible trajectory formats (Binpos,Crd,DCD,NetCDF).
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Plot Radius of Gyration along the trajectory
Programs: Ptraj from AmberTools package (Binpos,Crd,DCD,NetCDF trajectory formats). g_gyrate from Gromacs package (XTC trajectory format).
- Possibility to select a subset of atoms/residues from the whole system.
- User defined Mask only available for ptraj-compatible trajectory formats (Binpos,Crd,DCD,NetCDF).
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