Create various versions of a 3D variability result that can be used for display. Read a tutorial here.
Particles (from 3D Variability Analysis)
Volume (from 3D Variability Analysis)
simple mode: output a simple linear "movie" of volumes along each dimension. Number of frames is the next param.
cluster mode: fit clusters to reaction coordinates and output volumes and particles from each cluster. Number of clusters is the next param.
intermediates mode: reconstruct multiple intermediate volumes along each variability dimension, useful for better visualizing non-linear changes. Number of intermediate frames is the next param.
Intermediates: window (frames):
Size of rolling window in each bin (in number of frames). Set to a positive integer to define a triangular weighting function for each volume. Set to 0 for a tophat weighting function. Set to -1 to create bins with equal number of particles.
Volume series of each variability component
[Optionally] particles for each cluster or intermediate frame
[Optionally] volume for each cluster or intermediate frame
Common Next Steps
Visualization of results through UCSF Chimera or similar.