Bsoft program

jviews

Usage: jviews [options] [input.star]

Creates and modifies particle views.

Parameters:

-EvenOutput evenly distributed views.
-AsymmetricunitOutput all views within asymmetric unit.
-Grid10 Output all views within angular distance from a given reference view.
-RelatedOutput all symmetry related views for a given reference view and symmetry.
-Radial75,75,75 Generate a view vector for each particle extending from the given point.
-Top200 Assing one of the two top views (up/down) for each particle, depending if the particle is above or below the chosen Z slice.
-SegmentGenerate a view vector for each particle extending from the closest point on a line segment (defined as a filament in the input.star).
-Filament100,10,5 Generate views covering a filament with a given radius, helical rise & twist (use with option -symmetry)
and input.star defining the ends of a filament.
-Random100 Generate a number of random views.
-randomizealphaRandomize the angle around view vector (alpha).
-symmetryC10 Symmetry to use (default: C1 symmetry).
-recfile3d.map Associate views with this reconstruction filename.
-angle2 Angular sampling stepsize for theta and phi (default: 45 degrees).
-radius75 Place particles views at given radius (default 0).
-shift5 Shift particles by given amount along the view vectors (default 0).
-verbose7 Verbosity of output.
-reference0,0.618,1,0 Reference view (dafault: 0,0,1,0)
-sampling1.5,1.5,1.5 Sampling (A/pixel; a single value can be given).
-origin110,50,44 View origin (default: 0,0,0).
-discardz20 Discard views with Z locations further from the Z origin (pixels).
-select1 Process only particles with this selection number (default: all).
-invertInvert views in outputfile.
Chimera parameters:
-diameter5 Chimera marker diameter (default: 2)
-length100 Chimera link length (default: 10).
-thickness5 Chimera link thickness (default: 2)
-color0,0,1 Chimera marker & link color in RGB (default: 1,1,1).
-fomcolor0.2,0.3 Chimera marker & link coloring range from blue to red based on particle FOM.

Output:

-outputoutput.star Output parameter file
-cmmoutput.cmm Output Chimera marker file.
-pdboutput.pdb Output PDB file with BIOMT matrixes.

Bsoft version 2.0.7-20200917 (64 bit)


Generated by bdoc.pl on Mon Oct 26 08:20:12 2020


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