Bsoft program

bfind

Usage: bfind [options] input.img/input.star output.img

Searches orientation space for the best fit of a 3D map to a template.
Modes: Global: Search an asymmetric unit with a fixed angular step size. Directional: Do a search around a view within an angular distance (-limit option). Refine: Refine iteratively around a view to some accuracy (-accuracy option). Symmetry: Search all symmetry-related views using a given view. For modes other than global, the view is taken from the command line (-View option), or from the parameter file, or as a last resort from the image header. If a parameter file is used as input, the input image is selected based on the reconstruction ID and the particle image number. Only one image in a multi-image file will be used (see -image option). The output file contains the transformed map only if the input is an image (i.e., not a parameter file). Specify the output of the transformed map or template with the -particle and -newtemplate options.

Actions:

-global 2	Global search before other modes with binning.
-mode refine	Local modes: directional, refine or symmetric.
-setsequential	Set particle selection numbers sequentially.
-subset 25,5	View subset selection from a start offset and with a given size.
-rescale -0.1,5.2	Rescale output particle to average and standard deviation.

Parameters:

-verbose 7	Verbosity of output.
-datatype u	Force writing of a new data type.
-sampling 1.5,1.5,1.5	Sampling (A/pixel; default from input file; a single value can be given).
-origin 110,50,44	Template image origin (default taken from template file).
-partorigin 50,80,47	Particle image origin (default taken from particle file).
-angles 8.8,2.5,5.2	Step size for alpha, theta and phi, one value sets all (default 45 degrees).
-side 15	Generate side view projections within the given angle from the equator.
-resolution 15.6,200	Resolution limits for cross-correlation (default 0).
-shiftlimit 5.2	Radial limit to search for shift in cross-correlation map (default 1/4 of map).
-recid A435	The 3D reconstruction ID (should correspond to that in the parameter file).
-image 2	Image number in a multi-image file or particle number (default 1=first image).
-select 5	Particle selection number in parameter file (default not used).
-bin 3	Binning of input, template and mask by given kernel size,
	output image remains same size as input (only for local modes).

Parameters for the global and symmetric modes:

-symmetry D6	Symmetry: Point group identifier.

	Paramweters for the directional and refinement modes:
-View 0.3,-0.5,0.8,33	View to initiate search: vector {xyz} and angle.

Parameters for the directional mode:

-limit 17.5	Radial limit around given view (default 20 degrees).

Parameters for the refinement mode:

-accuracy 0.3	Smallest angle step size (default 0.5 degrees).

Input:

-Template image.map	Template to search for.
-mask rs_mask.mrc	Mask in real space to apply before cross-correlation.
-Mask fs_mask.mrc	Mask in reciprocal space to apply during cross-correlation.

Output:

-Postscript plot.ps	Output postscript file with a plot of global view vectors.
-output file.star	Parameter output file with best orientation.
-ppx	Write temporary particle parameter files to directory "ppx".
-json file.json	JSON single particle output file with best orientation.
-particle newpart.pif	New transformed particle file.
-newtemplate newtemp.pif	New transformed template file.

Bsoft version 2.0.7-20200917 (64 bit)

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

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