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3D Variability Estimation: Calculate 3D variability using a set of aligned projection images as an input.
Usage in command line
sx3dvariability.py prj_stack --output_dir=DIRECTORY --var3D=FILE_NAME --ave3D=FILE_NAME --img_per_grp=NUM_OF_IMAGES --sym=SYMMETRY --CTF --fl=LPF_CUTOFF_FREQ --aa=LPF_FALLOFF_WIDTH --symmetrize --var2D=FILE_NAME --ave2D=FILE_NAME --VAR --no_norm --npad=PADDING_FACTOR --decimate=FACTOR --window=WINDOW_SIZE --nvec=NUM_OF_EIGENVECTORS --VERBOSE
sx3dvariability exists only in MPI version.
For asymmetric structure:
mpirun -np 64 sx3dvariability.py stack --var3D=var_vol.hdf --ave3D=vol.hdf --img_per_grp=100 --CTF --fl=0.25 --aa=0.1
For structures that have symmetries (e.g. c2):
sx3dvariability.py stack --symmetrize --sym=c2 mpirun -np 64 sx3dvariability.py bdb:sdata --var3D=var_vol.hdf --ave3D=vol.hdf --img_per_grp=100 --sym=c2 --CTF --fl=0.25 --aaf=0.1
The program calculates the variability observed in a collection of image projections. Structures with symmetry require preparing data before calculating the variability. The data preparation step would symmetrise the data and output a bdb:sdata for variability calculation. sx3dvariability.py can be slow.
Pawel A. Penczek
Category 1:: APPLICATIONS
sparx/bin/sx3dvariability.py
Alpha:: Under development
There are no known bugs so far.