SAMUEL scripts list

Last updated: 07/20/2013

(Underlined scripts are most frequently used.)

[A to B]

samalign_multiref.py
    Align a particle stack against a reference stack, and output a new aligned particle stack.
samautopick.py
    Calculate the particle positions from micrographs, based on a set of reference 2D class averages.
samavgalignedimg.py
    After projection matching (e.g. samrefine.py, samalign_multiref.py), average the particles that match the same reference.
sambadpixels.py
    Replace bad pixels with local surrounding pixels using SPIDER. (Better use samfixoutliner.py)
sambfactor.py
    Low pass filter and apply temperature factor to a single 3D volume using “bfactor.exe”.
sambin.py
    Bin a single or a set of images/volumes. (For 2D (stack), better use sampilcopy2d.py)
samboxparticle.py
    Box out particles from micrographs. (Better use sampilboxparticle.py)
[C]

samclasscas.py
    2D classification using correspondence analysis (CA S), k-means classification (CL KM) and MRA (AP SH).
samclassify2d.py
    2D classification using SPIDER "AP C".
samcleanup.py
    Delete all temporary files from SAM, SPIDER, em2em, etc.
samcopy2d.py
    Convert a single image, image stack, or a set of single images; stack and unstack images; extract images from an image stack to form a new stack. (Better use sampilcopy2d.py, except for (un)stacking)
samcopy3d.py
    Convert the format of a single 3D volume or a set of volume files.
samcopycoor.py
    Convert the format of a set of coordinate files between SPIDER, Ximdisply and EMAN Boxer format.
samcopydoc.py
    Copy, extract and/or combine specific data lines and/or columns from SPIDER or PLT document files.
samctf_apply2d.py
    Apply CTF to an image stack.
samctf_phaseflip.py
    Correct the phase (CTF) of (a set of) 2D image (stack).
samctfsetup.py
    Set up EM parameters (stored in file “samctfsetup.inp”) for other ctf-related SAM commands.
samctf_wiener.py
    Apply Wiener filter on (a set of) 2D image (stack) or 3D volume.
[D to F]

samdefocus.py [More info]
    Determine defocus values using “ctffind3.exe” and “ctftilt.exe”. Generate/convert FREALIGN *.par and SPIDER *.dat files.
samdiffpar.py
    Calculate the difference between two FREALIGN *.par files.
samdistang.py
    Calculate the angle distance for the (theta, phi) of each particle after alignment.
samfft2d.py
    Generate FFT of 2D images using PIL.
samfft2d_refine.py
    Projection matching refinement using direct 2D FFT.
samfilter_bw.py
    Low pass filter a single or a set of images/volumes using Butterworth filter.
samfilter_contvol.py
    Extract the connected volume(s). Low-pass filter the volume edge, and generate a set of volumes with gradually enlarged masks.
samfilter_fermi.py
    High-pass and/or low-pass filter a single or a set of images/volumes using Fermi filter.
samfixoutliner.py
    Remove the outliners on micrographs by averaging the neighbouring pixels (using PIL).
samfrealign.py
    A package of functions related to FREALIGN refinement and reconstruction.
samfsc.py
    Generate FSC curves from 2 half volumes after applying certain masks.
[G to L]

samhist.py
    Draw a histogram/correlation plot of data points, and extract the document lines according to the given value range(s).
saminfo.py
    Retrieve the header information of SPIDER/MRC/DM3 image file.
saminitialmodel_op.py
    Make a set of initial models using SPIDER "OP".
saminvert.py
    invert the contrast of 2D image (stack). (Better use sampilcopy2d.py)
samlistexc.py
    A set of functions related to selection list files.
samlrefine.py
    3D projection matching: SPIDER global search, followed by FREALIGN local refinement and reconstruction.
[M]

sammars2d_flip.py
sammars2d.py
    2D alignment of an image stack against reference stack: generate class averages using Multiple Alignment ReferenceS (MARS) and weighting.
sammars3d.py
    (Multiple) 3D alignment using Multiple Alignment ReferenceS (MARS): generate class averages before reconstruction.
sammergedoc.py
    Merge a set of document files into a single file.
sammergeframe.py
    Sum certain subframes of an dose-fractionation image stack.
sammergestack.py
    Merge a set of 2D image stacks into a single stack.
sammirror.py
    Mirror (a set of) 2D image, 2D image stack or 3D volume.
sammontage.py
    Pick some images from a stack and save the image numbers in a list file. (Better use SamViewer)
sammrefine.py
    3D projection matching refinement using SPIDER "AP SH", generate class averages for reconstruction, one particle can be grouped into more than 1 reference (class average).
[N to Q]

samnormal_bg.py
    Normalize image stack based on the edge background value.
samnormal_variance.py
    Normalize image stack based on the variance. (Better use sampilcopy2d.py)
sampicklines.py
    Pick lines (e.g. coordinates) from a set of document files acoording to a continuous selection file.
sampilboxparticle.py
    Box out particles from micrographs using PIL, and process the particles at the same time.
sampilcopy2d.py [More info]
    Convert a single image, image stack, or a set of single images to SPIDER/MRC format; extract images from an image stack to form a new stack; process the image at the same time.
sampilmars2d.py
    2D alignment of an image stack against reference stack: generate class averages using Multiple Alignment ReferenceS (MARS) and weighting, using PIL.
samplot_res.py
    Draw an FSC curve for SPIDER resolution file(s).
samprj3d.py
    Generate projections of a 3D volume, which can be compared with its matched reference projection side by side.
sampwr.py
    Generate power spectra from micrographs using SPIDER. (Better use samfft2d.py)
[R]

samrac.py
    Initial model building using "Random Angle Cloud": grouped 2D class averages start with random grouped angles, then use FREALIGN local refinement to get reconstruction and phase residues.
samradon_ali2d.py
    Similar to samalign_multiref.py, but do 2D alignment via Radon transform.
samradon_make2d.py
    Generate 2D Radon transform(s) for an image (stack).
samradon.py
    Similar to samrefine.py, but do 2D alignment via Radon transform to get the euler angles and XY shifts at the same time.
samradon_refine3d.py
    Refinement via 3D Radon transform. Get the euler angles and XY shifts at the same time.
samrctpar.py
    Integrate all RCT parameters into a single SPIDER/FREALIGN alignment result file.
samreadinp.py
    Print out the parameters in any SAM input file (*.inp).
samrefine.py
    3D projection matching refinement using SPIDER.
samrelion.py [More info]
    A package of functions related to RELION.
[S]

samsa3d.py
    Simulated annealing of grouped 2D class averages to find Euler angles in 3D, start with random grouped angles, then use FREALIGN local to get rec and presa.
samscalevalue.py
    Multiply specific column(s) of a SPIDER/PLT document file by a value.
samshift2d.py
    Translationally (XY) shift an image (stack) according to the provided values (in a document file).
samsrcc.py
    Search for symmetry axis of a 3D volume by calculating the cc values with self-rotation volumes.
samsumali3d.py
    Sum Alignment results in 3D using SPIDER "SA 3".
samsvcoset.py
    Functions related to a set of coordinate files.
samsym3d.py
    Rotate and/or apply symmetry on a (set of) volume(s).
[T to Z]

samtiltdiff.py
    Search for TiltAxis and TiltAngle to transform two angles.
samtree2d.py
    Reference-free 2D classification solely based on MRA cc values,  by splitting low-cc particles from the high-cc ones.
samwradon.py
    Refinement via 3D Radon transform.
samwrefine.py
    3D projection matching refinement using SPIDER, with WALK (to get finer results).