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pipeline:subtract:centershift

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## sp_signalsubtract centershift

Center Map : Center map of remaining density.

## Usage

Usage in command line

	sp_signalsubtract.py centershift --cvol1=map_center_1 --cvol2=map_center_2 --shiftparams=shift_parameters --diffimgs=images_to_subtract --outdir=output_subtraction_directory --volradius=map_radius --apix=pixel_size --verbosity=verbosity_level

## Typical usage

sp_signalsubtract comprises the steps needed to subtract masked regions from a map in order to focus on the remaining features from that map. There are six steps for this process (five within SPHIRE):

2. Locate regions to be subtracted

6. Center map of the remaining density :

sp_signalsubtract.py --mode centershift --cvol1=centered_halfmap_1 --cvol2=centered_halfmap_2 --shiftparams=meridien_parameters --diffimgs bdb:output_subtraction_directory#all_subtracted --outdir=output_subtraction_directory --apix=pixel_size --volradius=structure_radius

As inputs “–cvol1” and “–cvol2”, use the half-maps generated by the previous reconstruction step. For “–shiftparams”, use the Meridien parameters for the iteration used for those reconstructions. e.g., of the form “final_params_015.txt”. For “–diffimgs”, use the signal-subtracted image stack from above.

The reconstruction will be roughly centered by alignment to a Gaussian blob of radius specified by the flag “–volradius”. (Additional centering options will be provided in the future.) If the pixel size is provided (–apix), the units of radius will be assumed to be in Angstroms. If the pixel size is not provided, the radius will be assumed to be in units of voxels. If your structure is not globular, try the shortest dimension.

The output centered parameter file will be combine the Meridien parameters with the centering parameters. The output reconstruction will not use smear information, and may be noisier than the reconstruction from the previous step. Simply make sure that the centering was adequate. The better the centering, the smaller the required shifts will be in subsequent refinements.

## Input

#### Main Parameters

--cvol1
First map to average and center. (default None)
--cvol2
Second map to average and center. (default None)
--shiftparams
Meridien parameters to combine with centering parameters. (default None)
--diffimgs
Images from signal subtraction to reconstruct. (default None)
--outdir
Directory where outputs will be written. (default required string)
Radius to use for centering reconstruction. If the structure is not globular, try the shortest dimension. (default None)
--apix
Pixel size in Angstroms. (default None)

--verbosity
Verbosity level
Controls how much information will be written to the screen. (default 2)

## Output

vol001_average.hdf
Reconstruction of subtracted particles
vol002_inverted.hdf
Negative of above reconstruction, subtracted region shouldn't have significant densities
vol003_centered.hdf
Centered reconstruction
params004_to_be_centered.txt
Original parameters
params005_centered.txt
Parameters after centering
Reconstruction (filtered) before centering
Reconstruction after centering

## Description

Tapu Shaikh

### Keywords

Category 1:: APPLICATIONS

### Files

sphire/bin/sp_signalsubtract.py