Best Smear : Shows distribution of particle smear and obtain subset.

Usage in command line

	sp_bestsmear.py meridien_params output_directory --max_smear=maximum_smear --stack=input_stack --verbosity=verbosity --iter=iteration_num --threads=num_threads 

The “smear” is the number of reference images to which Meridien has found a correlation. The assumption behind this utility is that a lower smear corresponds to higher certainty.

The purpose of sp_bestsmear.py is to:

: show the distribution of smear number for an iteration of Meridien
: select a subset of the particles with the lowest smear number

Distribution with no cutoff

1. Show the distribution of smear number:

sp_bestsmear.py meridien_params output_directory  

The main output is a distribution of the smear over the particle set.

2. Select a subset of the particles with the lowest smear:

sp_bestsmear.py meridien_params output_directory --max_smear=999 --stack=bdb:input_stack

Distribution before (top) and after (bottom) cutoff

If no input stack is provided, then only the plots, selection files, etc., will be written.

meridien_params

Parameter file from Meridien. (default required string)

output_directory

Toplevel directory where outputs will be written. (default required string)

--max_smear

Maximum smear number to allow. (default None)

--stack

Particle stack from which subset will be selected. (default None)

--verbosity

Controls how much information will be written to the screen. (default 3)

--iter

Iteration number from Meridien

Only necessary if the Meridien parameter filename can't be parsed. (default None)

--threads

Number of parallel threads used during Meridien

Will be determined automatically if not specified. (default None)

plot_smear.png

Plot of smear distribution(s)

bdb:bestsmear

Stack of selected particles

Tapu Shaikh

Category 1:: APPLICATIONS

sphire/bin/sp_bestsmear.py

Beta:: Under evaluation and testing. Please let us know if there are any bugs.