py4sci

Manual

Spring3d

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Spring3d - suite of programs that reconstruct 3D images from segmented helical particles

Program to iteratively refine 3D structure of helical specimens from segment stacks

Program to compute 3D reconstruction from a single class average using a range of different helical symmetries

Program to interactively explore grid searches according to different criteria

Program to plot refinement parameters from segmentrefine3d

Program to interactively explore refinement cycle statistics

Program to optimize segmentrefine3d reconstruction by varying refinement parameters systematically on a grid

Program to interactively inspect 3D reconstructions from segmentrefine3d using slice viewer

Program to assign a series of 3D models to class averages

Program to iteratively refine multiple 3D structures of helical specimens competitively from segment stacks

Spring2d

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Spring2d - suite of programs that analyze two-dimensional images of helices

Program to extract overlapping segments from micrographs

Program to examine all excised in-plane rotated segments and compute their collapsed (1D) and 2D power spectrum and width profile of helices

Program to classify excised in-plane rotated segments using SPARX’s k-means clustering

Program to align segments from helical specimens with a restrained in-plane rotation of 0 or 180 +/- delta degrees

Program to examine helix classes to compute their collapsed (1D) and 2D power spectrum and width profile of helices

Program to extract amplitudes and phases from desired layer lines of class averages

Program to simulate helical diffraction pattern and plot helical lattice from a series of indexed layer lines or rise/rotation parameters

Program to plot parameters from segmented helices

Springmicrograph

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Springmicrograph - suite of programs that work with micrographs

Program to split large scan into individual micrographs. The location of individual micrographs is determined by a dummy micrograph reference.

Program to examine micrograph quality by computing a localized power spectrum using EMAN2’s e2scaneval.py and an averaged power spectrum from overlapping tiles using SPARX’ sx_welch_pw2.py

Program to trace helices from micrographs

Program to determine CTF parameters from a set of micrographs using CTFFIND and CTFTILT (Mindell and Grigorieff JSB, 2003)

Program to evaluate the performance of scanner by correlating adjacent rows and lines with each other from a pure noise image.

Program to evaluate performance of scanner by measuring dots spaced 2.5 mm apart.

Program to evaluate scanner performance of scanner by measuring deviation from 45 degree line to determine CCD curvature and pincushion parameter.

Indices and tables