Package: scipion-em-cryosparc2
cryoSPARC2 pluginThis plugin allows to use cryoSPARC2 programs within the Scipion frameworkCryoSPARCis a backend and frontend software system
that provides data processing and image analysis capabilities for single particle
cryo-EM, along with a browser based user interface and command line tools.You will need to use3.0.0version of Scipion to run these protocols.2D Classification: Classify particles into multiple 2D classes to facilitate stack cleaning and removal of junk particles.  Also useful as a sanity check to investigate particle quality.3D Ab-Initio Reconstruction:  Reconstruct a single (homogeneous) or multiple (heterogeneous) 3-D maps from a set of particles, without any initial models or starting structures required.Particle Subtraction: Subtract projections of a masked volume from particles.Heterogeneous Refinement: Heterogeneous Refinement simultaneously classifies particles and refines structures from n initial structures, usually obtained following an Ab-Initio ReconstructionLocal CTF Refinement (per-particle defocus): Local CTF Refinement performs per-particle defocus estimation for each particle in a dataset, against a given 3D reference structure.Global CTF Refinement (per-group beam tilt, trefoil, spherical aberration, tetrafoil): Global CTF Refinement performs per-exposure-group CTF parameter refinement of higher-order aberrations, against a given 3D reference.Sharppening: Sharpen a volume following refinement.Helical 3D Refinement: Reconstruct and refine a homogeneous helical assembly, with or without imposition and refinement of symmetry parameters.3D Homogeneous Refinement(new): Rapidly refine a single homogeneous structure to high-resolution and validate using the gold-standard FSC. Using new faster GPU code, and support for higher-order aberration (beam tilt, spherical aberration, trefoil, tetrafoil) correction and per-particle defocus refinement on the fly.3D Non uniform Refinement(new): Apply non-uniform refinement to achieve higher resolution and map quality. Specially designed for small proteins and membrane proteins.3D Local Refinement(new)Refine a masked region within a consensus structure by allowing particle alignments to vary only slightly.Symmetry Expansion: Duplicate particles around a point-group symmetry.Homogeneous Reconstruction: Reconstruct half-maps from input particles with alignments3D Classification: Classify particles into multiple 3D classes and optimize 3D class densities (currently, without re-aligning particle pose or shift).3D Variability Analysis: Protocol to compute the principle modes of variability with a dataset of aligned particles3D Variability Display: Protocol to create various versions of a 3D variability result that can be used for displayBlob Picker: Automatically picks particles by searching for Gaussian signals.Patch CTF Estimation:  Patch-based CTF estimation automatically estimates defocus variation for tilted, bent, deformed samples and is accurate for all particle sizes and types including flexible and membrane proteins.Latest plugin versionv4.0.10newCompatibility with cryoSPARC v4.4.1newAdd new protocols:3D Variability Analysis: Protocol to compute the principle modes of variability with a dataset of aligned particles3D Variability Display: Protocol to create various versions of a 3D variability result that can be used for displayBlob Picker: Automatically picks particles by searching for Gaussian signals.v4.0.9newCompatibility with cryoSPARC v4.4.0fixedHandling aborted protocols/jobsInstalling the pluginIn order to install the plugin follow these instructions:Install the pluginscipion installp -p scipion-em-cryosparc2or through theplugin managerby launching Scipion and followingConfiguration>>PluginsInstallCryoSPARC softwareCryoSPARC v2 software willNOTbe installed automatically with the plugin. The
independent installation of CryoSPARC software suite by the user is required
before running the programs.To install CryoSPARC v2 software review the detailed system requirements and install
instructions availablehere.
These cover workstation and cluster installs, file configuration and how to update
cryoSPARC v2 when new versions become available.Add the following variables to the scipion config file (run scipion3 config –show to open it)# The root directory where cryoSPARC code and dependencies is installed.
CRYOSPARC_HOME = <install_path>   (CRYOSPARC_DIR will work for legacy reasons)

# full name of the initial admin account to be created
CRYOSPARC_USER = <user_name>

# Optional variables

#Folder (available to all workers) where scipion will create cryosparc projects
CRYO_PROJECTS_DIR = <path> (default to <CRYOSPARC_HOME>/scipion_projects)

# Specifies whether the CS installation is standalone or not. If False,
# it is assumed that CS is installed in a cluster. If the variable is not
# defined, by default assume that the installation is standalone and its
# value would be True
CRYOSPARC_STANDALONE_INSTALLATION = <True or False>

# Name of the default lane where the protocols will be launched
CRYOSPARC_DEFAULT_LANE = <lane name>To install in development modeClone or download the plugin repositorygit clone https://github.com/scipion-em/scipion-em-cryosparc2.gitInstall the plugin in developer mode.scipion installp -p local/path/to/scipion-em-cryosparc2 --develBuildbot statusStatus devel version:Status production version: