Bsoft program

bmgalign

Aligns micrographs within sets such as focal series specified in parameter files.

-align mic	Alignment type: par = particle coordinates, mic = micrograph images, fea = micrograph features.
-add	Add micrograph coordinates and particle origins (default not).
-filterextremes	Filter micrograph extremes before aligning.

-verbose 7	Verbosity of output.
-number 3	Number of micrographs per field-of-view (default 1).
-fieldID dbgd	Set the field ID (multiple micrographs will get numbered ID's).
-reference 2	Reference micrograph in a series (default 1=first micrograph).
-datatype u	Force writing of a new data type.
-sampling 1.5,1.5,1.5	Sampling (A/pixel; a single value can be given).
-correlate 1024,1024,5	Size of subimages for correlation (default 512,512,1, use with -align mic).
-resolution 900,300	High and low resolution limits for bandpass (default 0.1,1000 angstrom).
-maxshift 55	Maximum allowed shift (default 1/4 of tile).
-threshold -3.0	Threshold used to pick features (in std dev units; default -3, use with -align fea).
-features 1,55	Features type (1=mass, 2=area, 3=darkest pixel) and maximum number (default 1,unlimited).

-output file.star	Output parameter file.
-image file.pif	Output multi-image file with aligned images.

	The set of input files reference a series of micrographs arranged in
	fields-of-view where each field contains a focal pair or set. The program then
	calculates for each set the alignment of all other micrographs with respect
	to the reference micrograph (typically the further-from-focus micrograph),
	and outputs a new STAR format file with the alignment parameters and particle
	coordinates corresponding to the alignment. The alignment can be done in
	three different ways:
	1. Alignment by cross-correlation (recommended):
	bmgalign -v 7 -reference 2 -align mic -correlate 300,300,1 -out out.star input.star
	2. Alignment by feature extraction:
	bmgalign -v 7 -ref 2 -resol 300,1000 -align fea -thresh -2.8 -out out.star input.star
	3. Alignment using picked particle coordinates:
	bmgalign -v 7 -ref 2 -align part -output out.star input.star

	All input is derived from a STAR format parameter file.
	A series (such as a focal pair) is assumed to be consecutive data blocks in the STAR file.
	Orientational parameters are calculated so that applying them to the first
	data set or image produces the others in the focal series.
	Angles are given with positive counter-clockwise.

Bsoft version 2.0.7-20200917 (64 bit)

Generated by bdoc.pl on Mon Oct 26 08:20:11 2020