Name

sxvar.py - calculate 3D variance for a set of bootstrap volume files

Usage

usage in command line

mpirun -np 4 sxvar.py bootstrap/bsvol000*.hdf variance --fl=0.2 --aa=0.1 --radccc=24 --MPI

usage in python programming

var(prefix, nfile, nprj, output, fl, fh, radccc, writelp, writestack)

Typical usage

mpirun -np 4 sxvar.py bootstrap/bsvol000*.hdf variance --fl=0.2 --aa=0.1 --radccc=24 --MPI

Input

prefix

the prefix of the set of volume stacks generated by sxbootstrap_bigdisk.py

fl,aa

the parameters of the low pass filtration using filt_tanl.

radccc

radius for calculating cross correlation coefficient and masking the 3D variance.

writelp

whether write the low-pass filtered volumes to the disk.

writestack

whether write the intermediate results (odd, even and all variance map for every 100 volumes).

Output

outputfile

the average and variance maps will be saved in current directory as avg.hdf and var.hdf.

Description

• The parameters of low-pass filtration is suggested to be set to around half of the frequency while FSC reaches 0.5. For example,

if FSC reaches 0.5 at frequency 0.3, fl and fh should be around 0.15, and the distance between them is suggested to be about 0.05.

• This is fourth step of the real-space variance calculations.

Method

Reference

Author / Maintainer

Wei Zhang

Keywords

category 1

APPLICATIONS

Files

sparx/bin/sxnormal_prj.py

See also

sxali3d_e

Maturity

beta

works for author, often works for others.

Bugs

Did not discover any yet.