Name

sx3dvariability.py - calculate 3D variability field using a set of aligned 2D projection images as an input. The structures with symmetry require preparing data before calculating variability. The data preparation step would symmetrize the data and output a bdb:sdata for variability calculation.

Usage

usage in command line

for asymmetric structure:

mpirun -np 472 sx3dvariability.py stack --CTF --img_per_grp=100 --fl=0.25 --aa=0.1 --ave3D=vol.hdf --var3D=var_vol.hdf --decimate=2 --window=180

for structures that have symmetries:

sx3dvariability.py stack --symmetrize --sym=c2

mpirun -np 472 sx3dvariability.py bdb:sdata --CTF --img_per_grp=100 --fl=0.40 --aa=0.1 --ave3D=vol.hdf --var3D=var_vol.hdf --sym=c2 --decimate=2 --window=180

Input

stack: stack of 2D images with 3D orientation parameters in header and (optionally) CTF information
img_per_grp: number of projections from the angular neighborhood that will be used to estimate 2D variance for each projection data. The larger the number the less noisy the estimate, but the lower the resolution. Usage of large number also results in rotational artifacts in variances that will be visible in 3D variability volume.
fl: the cut-off frequency of the low pass filter to be applied to 2D data prior to variability calculation (default - no filtration).
aa: the fall-off frequency of the low pass filter to be applied to 2D data prior to variability calculation (default - no filtration).
symmetrize: specified in case the input structure has symmetry higher than c1. It is specified together with option --sym in the first step for preparing data. Notice this step can be run with only one CPU and there is no MPI version for it.
decimate: Image decimate rate. In case both the number and size of the images are large, it is required to reduce the size of image to conduct a successful run. Option decimate is a float number that is larger than one.
window: In case image size is not properly chosen, remove margin area.

Output

bdb:sdata: symmetrized data for 3D variability analysis whereas the reconstructed structure has symmetry that is higher than c1. It is output of the first step and input of the second step.
ave3D: 3D reconstruction computed from projections averaged within respective angular neighborhood. It should be used to assess the resolvability and possible artifacts of the variability map.
var3D: 3D variability map

Description

It can be slow. Window is applied before decimation. So the chosen window size is related to the original image size.

Method

Reference

Author / Maintainer

Pawel Penczek

Keywords

category 1: APPLICATIONS

Files

sx3dvariability.py

Maturity

alpha: it works.

Bugs

Did not discover any yet.