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"author": "Szu-Chi Chung, Yunior C. Fonseca Reyna",
"author_email": "phonchi@stat.sinica.edu.tw, cfonseca@cnb.csic.es",
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"description": "=================\ncryoSPARC2 plugin\n=================\n\nThis plugin allows to use cryoSPARC2 programs within the Scipion framework\n\n`CryoSPARC `_ is a backend and frontend software system\nthat provides data processing and image analysis capabilities for single particle\ncryo-EM, along with a browser based user interface and command line tools.\n\nYou will need to use `2.0.0 `_ version of Scipion to run these protocols.\n\n* **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.\n* **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.\n* **3D Homogeneous Refinement**: Rapidly refine a single homogeneous structure to high-resolution and validate using the gold-standard FSC.\n* **3D Non uniform Refinement**: Apply non-uniform refinement to acheive higher resolution and map quality\n* **Particle Subtraction**: Subtract projections of a masked volume from particles.\n* **3D Local Refinement** Naive local refinement.\n\n**Installing the plugin**\n=========================\n\nIn order to install the plugin follow these instructions:\n\n1. **Install the plugin**\n\n.. code-block::\n\n scipion installp -p scipion-em-cryosparc2\n\nor through the **plugin manager** by launching Scipion and following **Configuration** >> **Plugins**\n\n\n2. Install **CryoSPARC software**\n\nCryoSPARC v2 software will *NOT* be installed automatically with the plugin. The\nindependent installation of CryoSPARC software suite by the user is required\nbefore running the programs.\n\nTo install CryoSPARC v2 software review the detailed system requirements and install\ninstructions available `here `_.\nThese cover workstation and cluster installs, file configuration and how to update\ncryoSPARC v2 when new versions become available.\n\n3. Add the following variables bellow the PACKAGES section at ``~/.config/scipion/scipion.conf`` file:\n\n .. code-block::\n\n # The root directory where cryoSPARC code and dependencies will be installed.\n CRYOSPARC_DIR = \n \n # full name of the initial admin account to be created\n CRYOSPARC_USER = \n \n # path on the worker node to a writable directory residing on the local SSD\n CRYOSSD_DIR = \n\n\n\n\n\n**To install in development mode**\n\n- Clone or download the plugin repository\n\n.. code-block::\n\n git clone https://github.com/scipion-em/scipion-em-cryosparc2.git\n\n- Install the plugin in developer mode.\n\n.. code-block::\n\n scipion installp -p local/path/to/scipion-em-cryosparc2 --devel",
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