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This version (2021/10/11 17:13) was approved by shaikh.

Generate and Apply Mask : Make a soft mask of the region to be excluded.

## Usage

Usage in command line

    sp_signalsubtract.py sp_mask --map2mask=map_to_make_mask_from --fullmap=full_map --outdir=output_subtraction_directory --mapthresh=threshold --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

3. Mask a soft mask of the region to be excluded :

sp_signalsubtract.py sp_mask --map2mask=map_to_make_mask_from --outdir=output_subtraction_directory --fullmap=full_map --mapthresh=threshold


The map to make a mask from (–map2mask) corresponds to the region that you want to subtract.

!!!IMPORTANT!!! The full map which is to be multiplied by the mask (–fullmap) must NOT have been postprocessed (e.g., sharpened). Otherwise, re-projections will not be optimally comparable to the experimental images.

Grouped segments

## Input

#### Main Parameters

Map from which a mask will be generated. (default required string)
--fullmap
Map which will be multiplied by the mask. (default None)
--outdir
Directory where outputs will be written. (default required string)
--mapthresh
Full map will be initially binarized at this threshold. (default None)

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

## Output

ctf_params.txt
CTF parameter file

## Description

Tapu Shaikh

### Keywords

Category 1:: APPLICATIONS

### Files

sphire/bin/sp_signalsubtract.py