Job: 3D Variability Display

3D variability display.

Description

Create various versions of a 3D variability result that can be used for display. Read a tutorial here.

Input

• Particles (from 3D Variability Analysis)

• Volume (from 3D Variability Analysis)

Common Parameters

• Output mode:

  • 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.

Output

• 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.