Segrefine3dinspect¶
Program to interactively inspect 3D reconstructions from segmentrefine3d using slice viewer
Input: Volume reconstruction
Output: Interactive screenshot
Parameters¶
Parameter |
Example (default) |
Description |
|---|---|---|
Volume reconstruction |
recvol_1223apix.hdf |
Untreated 3D reconstruction to be inspected: accepted image file formats (hdf). |
Batch mode |
False |
Batch mode for plot. Otherwise interactive. |
Estimated helix inner and outer diameter in Angstrom |
(0, 190) |
Generous inner and outer diameter of helix required for cylindrical mask in Angstrom (accepted values min=0, max=1500). |
Pixel size in Angstrom |
1.163 |
Pixel size is an imaging parameter (accepted values min=0.001, max=100). |
Helical rise/rotation or pitch/number of units per turn choice |
rise/rotation |
Choose whether helical ‘rise/rotation’ or ‘pitch/unit_number’ of units per turn pairs are given for generating the helical lattice. |
Helical symmetry in Angstrom or degrees |
(1.408, 22.03) |
Helical rise/pitch (Angstrom) and rotation (degrees)/number of units per turn to be imposed to 3D reconstruction (accepted values min=-1000, max=1000). |
Sample parameter file¶
You may run the program in the command line by providing the parameters via a text file:
segrefine3dinspect --f parameterfile.txt
Where the format of the parameters is:
Volume reconstruction = recvol_1223apix.hdf
Batch mode = False
Estimated helix inner and outer diameter in Angstrom = (0, 190)
Pixel size in Angstrom = 1.163
Helical rise/rotation or pitch/number of units per turn choice = rise/rotation
Helical symmetry in Angstrom or degrees = (1.408, 22.03)
Additional parameters (intermediate level)¶
Parameter |
Example (default) |
Description |
|---|---|---|
Output volume name |
recvol.hdf |
Output name for processed volume: accepted image file formats (hdf). |
B-factor |
True |
Option to apply a B-factor to the structure. |
B-factor and resolution cutoff |
(-200.0, 5.0) |
B-factor in 1/Angstrom^2 and resolution cutoff in Angstrom (accepted values min=-10000, max=10000). |
Real-space mask |
True |
Option to apply a real-space mask of choice to the structure. |
Mask type |
cylinder |
Type of real-space mask to apply: a cylinder mask based on the provided inner and outer width of structure or a general structural mask based on thresholding. |
Rotational symmetry |
1 |
Additional x-fold rotational symmetry or x-number of helix start (accepted values min=1, max=100). |
Helix polarity |
polar |
Choose whether helix is ‘polar’ or ‘apolar’. Polar helices have different ends at the top and bottom. Only the predominant direction within a helix will be used for the reconstruction. In apolar helices they are related by 180 degree rotation. Thus each segment can be inserted twice in the 3D reconstruction in opposite directions. |
Sample parameter file (intermediate level)¶
You may run the program in the command line by providing the parameters via a text file:
segrefine3dinspect --f parameterfile.txt
Where the format of the parameters is:
Volume reconstruction = recvol_1223apix.hdf
Batch mode = False
Output volume name = recvol.hdf
B-factor = True
B-factor and resolution cutoff = (-200.0, 5.0)
Real-space mask = True
Mask type = cylinder
Estimated helix inner and outer diameter in Angstrom = (0, 190)
Pixel size in Angstrom = 1.163
Helical rise/rotation or pitch/number of units per turn choice = rise/rotation
Helical symmetry in Angstrom or degrees = (1.408, 22.03)
Rotational symmetry = 1
Helix polarity = polar
Additional parameters (expert level)¶
Parameter |
Example (default) |
Description |
|---|---|---|
Signal-to-noise weighting |
False |
Option to apply a signal-to-noise weighting based on FSC curve from Rosenthal and Henderson, 2003 J Mol Biol. This measure avoids amplification of noise. |
FSC curve |
fsc_curve.dat |
FSC curve corresponding to provided reconstruction: accepted file formats (dat, .db). |
Layer-line Fourier filter |
False |
Option to apply a Fourier filter at the positions of the layer lines. |
Long helix |
False |
Option to generate a long volume with helical symmetry imposed. Simultaneous application of B-factor/resolution cutoff and long helix option is discouraged as long helices undergo a series of shifts/rotations requiring interpolation. This operation results to an additional decay of amplitudes. Avoid additional sharpening by generating and saving the long helix to a file and launch another run of SEGREFINE3DINSPECT to apply the B-factor and resolution cutoff to the elongated volume. |
Helix length in Angstrom |
1000 |
Helix length in Angstrom (accepted values min=0, max=10000). |
Swap handedness |
False |
Apply mirror operation to helix to swap handedness |
Sample parameter file (expert level)¶
You may run the program in the command line by providing the parameters via a text file:
segrefine3dinspect --f parameterfile.txt
Where the format of the parameters is:
Volume reconstruction = recvol_1223apix.hdf
Batch mode = False
Output volume name = recvol.hdf
B-factor = True
B-factor and resolution cutoff = (-200.0, 5.0)
Signal-to-noise weighting = False
FSC curve = fsc_curve.dat
Real-space mask = True
Mask type = cylinder
Layer-line Fourier filter = False
Estimated helix inner and outer diameter in Angstrom = (0, 190)
Pixel size in Angstrom = 1.163
Helical rise/rotation or pitch/number of units per turn choice = rise/rotation
Helical symmetry in Angstrom or degrees = (1.408, 22.03)
Rotational symmetry = 1
Helix polarity = polar
Long helix = False
Helix length in Angstrom = 1000
Swap handedness = False
Command line options¶
When invoking segrefine3dinspect, you may specify any of these options:
usage: segrefine3dinspect [-h] [--g] [--p] [--f FILENAME] [--c] [--l LOGFILENAME] [--d DIRECTORY_NAME] [--version] [--batch_mode] [--b-factor]
[--signal-to-noise_weighting] [--real-space_mask] [--layer-line_fourier_filter] [--long_helix] [--swap_handedness]
[input_output [input_output ...]]
Program to interactively inspect 3D reconstructions from segmentrefine3d using slice viewer
positional arguments:
input_output Input and output files
optional arguments:
-h, --help show this help message and exit
--g, --GUI GUI option: read input parameters from GUI
--p, --promptuser Prompt user option: read input parameters from prompt
--f FILENAME, --parameterfile FILENAME
File option: read input parameters from FILENAME
--c, --cmd Command line parameter option: read only boolean input parameters from command line and all other parameters will be assigned
from other sources
--l LOGFILENAME, --logfile LOGFILENAME
Output logfile name as specified
--d DIRECTORY_NAME, --directory DIRECTORY_NAME
Output directory name as specified
--version show program's version number and exit
--batch_mode, --bat Batch mode for plot. Otherwise interactive. (default: False)
--b-factor, --b-f Option to apply a B-factor to the structure. (default: False)
--signal-to-noise_weighting, --sig
Option to apply a signal-to-noise weighting based on FSC curve from Rosenthal and Henderson, 2003 J Mol Biol. This measure
avoids amplification of noise. (default: False)
--real-space_mask, --rea
Option to apply a real-space mask of choice to the structure. (default: False)
--layer-line_fourier_filter, --lay
Option to apply a Fourier filter at the positions of the layer lines. (default: False)
--long_helix, --lon Option to generate a long volume with helical symmetry imposed. Simultaneous application of B-factor/resolution cutoff and
long helix option is discouraged as long helices undergo a series of shifts/rotations requiring interpolation. This operation
results to an additional decay of amplitudes. Avoid additional sharpening by generating and saving the long helix to a file
and launch another run of SEGREFINE3DINSPECT to apply the B-factor and resolution cutoff to the elongated volume. (default:
False)
--swap_handedness, --swa
Apply mirror operation to helix to swap handedness (default: False)
Program flow¶
apply_structural_mask_if_demanded: Generate and apply structural mask
apply_layerline_filter_if_demanded: Generate and apply layer-line filter
apply_bfactor_if_demanded: Apply B-factor