Manual¶
Spring3d¶
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¶
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¶
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 optimize michelixtrace by varying michelixtrace parameters systematically on a grid
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.