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jspr

jspr (/ˈjaspər/) is a collection of the programs for single particle cryo-EM image processing and 3-D reconstruction that are developed in Wen Jiang group in the Department of Biological Sciences, Purdue University.

Major Features

  • Support for all point-group symmetries including all platonic solids (icosahedral, octahedral, and tetrahedral symmetries), dihedral symmetry (Dn), cyclic symmetry (Cn), and no symmetry (C1).
  • Asymmetric reconstruction of structures with mixed symmetries
    • standard asymmetric reconstruction (SAR, i.e. all components are identically arranged in all particles)
    • focused asymmetric reconstruction (FAR, i.e. all components have defined structure but can be arranged differently in different particles)
  • De novo initial model
    • random model approach
    • synthetic shapes (icosahedra and dodecahedra with adjustable size, shell thickness, and curvature)
  • Truly independent reconstruction (initial model and refinement) and “gold” standard resolution evaluation with automated mask size/slope optimization
  • Support merging of multiple datasets imaged using different microscopes or at different magnifications
  • Support small to very large maps (864^3 so far) and datasets (10^5 particles)
  • Refinement and correction of elliptic distortion without the need for pre-calibration of the microscope using polycrystal samples
  • Many filters to choose a subset of particles for inclusion in 3-D reconstruction
    • consensus approach: consistent views from multiple independent refinements
    • stable solution approach: stable views from multiple iterations of refinements
    • resolution-dependent weighting by scores, defocus, etc. across all micrographs or for individual micrographs
  • High-resolution refinements (used to solve several near-atomic resolution structures of viruses, protein complexes, and helical tubes/filaments)
    • grid-less optimization of particle view/position parameters
    • defocus and astigmatism refinement
    • beam tilt refinement
    • magnification refinement
    • anisotropic magnification (elliptic distortion) refinement
    • simultaneous refinement of any combination of these parameters (refineAll aligner)
  • Parallel processing
    • Computers
      • single desktop/workstation with multi-cores
      • collection of workstations
      • clusters
      • distributed computer nodes pooled using HTCondor
    • Job queues
      • ad-hoc without queues
      • PBS/Torque/Slurm etc.
      • HTCondors
    • Parallel 3-D reconstruction using MPI with adaptive workload assignment for nodes of different performances
  • Utility tools
    • text-based virtual image format (.lst)
      • create very large datasets from multiple micrographs while keeping the file small
      • storage of arbitrary parameters using key=value pairs
      • flexible operations of datasets: merge, split, common, difference, etc. (images2lst.py)
      • all these flexible operations without the need to modify the actual binary image files
    • interconversion of cryoSPARC cs files, Relion star files (including the new format with an optical group section), and jspr lst files (images2lst.py, images2star.py)
    • automated masking and calculation of “true” FSC (trueFSC.py)
    • plotting particle parameters including single parameter histogram, pair-wise parameter correlations, etc. (plotDist.py)
    • determine helical parameters from a 3D map (helicalSym.py)
    • many other utilities (images2lst.py, images2star.py)

Mailing List

Please use the jspr Google Group as the mailing list to ask questions and post answers.

Documentations

References

This software is built on top of EMAN and EMAN2 with many additions and bug fixes. Please cite the following references in your publication:

Download and Installation

  • Linux x86_64 package: jspr.python3.2020-5-14.tar.gz (2.1 GB). Compiled on a Centos 7 64-bit Linux system with GNU G++ version 8.4.0.
    New feature: the first version that uses python 3.7
    Download and then unpack it. All contents will be unpacked into folder jspr. Please follow the instructions in jspr/README to use the software.

Older versions
  • Linux x86_64 package: jspr.2019-12-5.tar.gz (1.26 GB). Compiled on a Centos 7 64-bit Linux system with GNU G++ version 8.4.0. It will be the last version using Python 2.7.
    New feature: refineAll aligner; trueFSC.py; helicalSym.py; support for Slurm queue
    Download and then unpack it. All contents will be unpacked into folder jspr. Please follow the instructions in jspr/README to use the software.
  • Linux x86_64 package: jspr.2018-10-25.tar.gz (1.36 GB) 
    Download and then unpack it. All contents will be unpacked into folder jspr. Please follow the instructions in jspr/README to use the software.
  • Linux x86_64 package: jspr.2017-7-20.tar.gz (598.4 MB) 
    New feature: conversion of jspr lst files from/to Relion star files 
    Download and then unpack it. All contents will be unpacked into folder jspr. Please follow the instructions in jspr/README to use the software.
  • Linux x86_64 package: jspr.2016-5-4.tar.gz (521.4 MB) 
    New feature: elliptic distortion refinement and correction 
    Download and then unpack it. All contents will be unpacked into folder jspr. Please follow the instructions in jspr/README to use the software.
  • Linux x86_64 package: jspr.2014-02-10.tar.gz (329 MB) 
    Download and then unpack it (for example, run tar zxvf cryoem.jspr.2014-02-10.tar.gz in a terminal). All contents will be unpacked into folder cryoem. Please follow the instructions in cryoem/README to use the software.