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Plugin to use IMAGIC programs within the Scipion framework

Project description

This plugin includes two protocols to provide wrappers around Multivariate Statistical Analysis (MSA) module of IMAGIC software suite. IMAGIC is a licensed software, not distributed with Scipion and has to be installed by user.

Installation

You will need to use 3.0 version of Scipion to be able to run these protocols. To install the plugin, you have two options:

  1. Stable version
scipion installp -p scipion-em-imagic
  1. Developer’s version

    • download repository
    git clone https://github.com/scipion-em/scipion-em-imagic.git
    
    • install
    scipion installp -p path_to_scipion-em-imagic --devel
    

Also, you need a working IMAGIC installation. Default installation path assumed is software/em/imagic-190830, if you want to change it, set IMAGIC_HOME in scipion.conf file to the folder where the IMAGIC is installed (it is the same as IMAGIC_ROOT variable in your shell environment). If you want to use MPI-based parallel job execution, make sure you have openmpi directory inside IMAGIC installation folder. To check the installation, simply run the following Scipion test:

scipion tests tests.em.workflows.test_workflow_imagicMSA.TestImagicWorkflow

Supported versions

  • 190830

Since with every version of IMAGIC software user interaction with IMAGIC programs is changed, we came up with a way to provide multiple version support. In imagic/scripts directory you have a folder for each corresponding version, that contains batch scripts similar to those used by IMAGIC. This way one can create a similar script specific to a certain version. At the moment version 190830 (Aug 2019) is supported. If you experience any problems or need help with adapting scripts for your IMAGIC version, do not hesitate to create an issue on Github. Besides editing scripts directory you would need to add version number to _supportedVersions list in file imagic/__init__.py and edit IMAGIC_HOME variable in scipion.conf.

Protocols

  • imagic - msa
  • imagic - msa-classify

References

  1. M van Heel and W Keegstra (1981). IMAGIC: A fast, flexible and friendly image analysis software system. Ultramicroscopy 7: 113-130.
  2. M van Heel, G Harauz, EV Orlova, R Schmidt and M Schatz (1996). A new generation of the IMAGIC image processing system. J. Struct. Biol. 116: 17-24.
  3. M van Heel, R Portugal, A Rohou, C Linnemayr, C Bebeacua, R Schmidt, T Grant and M Schatz (2012). Four-Dimensional Cryo Electron Microscopy at Quasi Atomic Resolution: “IMAGIC 4D”. International Tables for Crystallography, vol. F, ch. 19.9: 624-628.
  4. M van Heel (1984). Multivariate statistical classification of noisy images (randomly oriented biological macromolecules). Ultramicroscopy 13(1-2): 165-183.
  5. Lisa Borland and Marin van Heel (1990). Classification of image data in conjugate representation spaces. Journal of the Optical Society of America A 7(4): 601-610.

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