Bsoft program

bpartsel

Usage: bpartsel [options] input.star [input.star]

Selects single particles for reconstruction and further processing.

Input particle selections are honoured, so that multiple restrictive selections

can be made. To reset for a new selection, use the -all option.

Actions:

-checkCheck particle records.
-reconstructionsOperate on reconstruction parameters rather than micrographs.
-renumberRenumber particles starting from 1 for each micrograph or reconstruction.
-allReset selection to all particles before other selections.
-noneUnset selection to all particles before other selections.
-mgselect 3-5,8,12-15Select micrographs:
Argument: 4-11,34: Select by the indicated micrographs (first = 1).
Argument: part: Select only micrographs with selected particles.
-divide 3Divide the project into a number of subsets of fields.
-consolidate 5Consolidate selection under the given selection number.
-setnumber 3Select given selection number and set others to zero.
-setfom 0.3Set the FOM (must be in the range 0-1).
-setasu D3Set the views to the asymmetric unit.
-setgroupsTransfer selection numbers to groups.
-fixdefocus 0.15Reset particle defocus differing from micrograph defocus.
-group 3022Select particles belonging to this group.
-sets 20,1Generate sets of this size of selected particles,
with a flag not to select across micrograph or reconstruction boundaries.
-series 25,1Select: Particles that are all selected in a series and generating sets
with a flag not to select across micrograph or reconstruction boundaries.
-frames 3,11Select: Particles from a series of frames of a field-of-view.
-alternate 3Select: Assign successive particles to different numbers.
-reselect psi,0.1,0.9Reselect based on a range of values associated with this tag.
-origin 150,150,0,8Select: Within a distance from the nominal origin: x,y,z,distance.
-View 0.2,-0.5,0.3,15Select: Within an angular distance from a view: x,y,z,angle.
-sideview 17.8Select: Side views within an angular distance from the equator.
-Euler 2,50,-30,2,0,40Select: Euler angle ranges: psi, theta, phi.
-rank 4,1Select a number of groups from FOM ranking and flag to adjust for defocus.
-fom 0.25,1Select: FOM cutoff and flag to adjust for defocus.
-cv 0.55,1Select: Cross validation cutoff and flag to adjust for defocus.
-exclusion 210Select: Deselect overlapping particles (default 0).
-top 12.0,1Select: number or % particles and flag to adjust for defocus, ranked by FOM[index].
-deviation -2.0Select: FOM >= average + factor*standard_deviation, using FOM[index].
-angle 2.4Select: difference angle between view vectors in focal or tilt series.
-closesttofocusSelect: Particles from micrographs closest to focus.
-furthestfromfocusSelect: Particles from micrographs furthest from focus.
-random 23.6%Select: random selection to get the given number,
number in groups (g), fraction (<1) or percentage (%).
-bootstrap 527Select: random selection with replacement up to the given number.
-views 4.5,7.2,3Select: random selection within views defined on a grid with the
given theta and phi step sizes (degrees) and up to the given number.
-bestviews 4.5,7.2,3Select: best particles within views defined on a grid with the
given theta and phi step sizes (degrees), up to the given number.
-maxsmooth 0.7,3,5,4.4Select: above fraction specified by smoothed maxima surface.
given theta and phi step sizes and smoothing sigma (degrees).
-FomfirstSet orientations to first in field-of-view series.
-FombestSet orientations to best FOM[index] in field-of-view series.
-filament 60Selects filament particles with clear direction based on percentage.
-deselect 4,6,22Deselect particles with the listed selection numbers.
-getselectionPrints all the selection numbers.
-show particle.fomShow particle parameters indicated by the tag or selection number.
-Fomhistogram 100,0.1.2Show FOM histogram with parameters: bins, minimum and maximum.
-focusShow defocus minimum and maximum.
-reset defocusReset particle defocus to micrograph defocus.
-deleteDelete all non-selected particles from the parameter file.
-removeDo not write non-selected micrographs into the parameter file.

Parameters:

-verbose 7Verbosity of output.
-symmetry C5Point group symmetry (required with the -angle and -views options).
-index 1FOM index to select on (default 0, options -setfom, -top, -deviation, -bestviews, -Fombest).

Output:

-output file.starOutput parameter file.
-split 3Split micrograph or reconstruction data blocks into individual files:
Argument: 1-6: number of digits inserted before extension
Argument: "id": micrograph ID's are used as file names.
Argument: "set": particle sets based on selection are used as output.
-Particle views.psPostscript output with particle view and origin distributions.
-Micrograph out.psPostscript output with particle micrograph distributions.
-FOM histogram.psPostscript output with particle FOM distributions.
-classesWrite stacks of particle images based on classes.

Bsoft version 2.0.7-20200917 (64 bit)


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


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