scipion-em-spider 1.0.9

Plugin to use Spider programs within the Scipion framework

This plugin provide wrappers around several programs of SPIDER software suite.

Installation

You will need to use 2.0 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-spider

2. Developer’s version

   • download repository

   git clone https://github.com/scipion-em/scipion-em-spider.git

   • install

   scipion installp -p path_to_scipion-em-spider --devel

SPIDER binaries will be installed automatically with the plugin, but you can also link an existing installation. Default installation path assumed is software/em/spider-25.02, if you want to change it, set SPIDER_HOME in scipion.conf file to the folder where the SPIDER is installed. Additional information about using SPIDER with MPI can be found on a separate page. Unfortunately, at the moment we do not support MPI in our SPIDER wrappers, since it requires a lot of effort to refactor almost all protocols. :( Depending on you CPU type you might want to change the default binary from spider_linux_mp_intel64 to a different one by explicitly setting SPIDER variable. Similarly you can modify SPIDER_MPI variable (default spider_linux_mpi_opt64).

To check the installation, simply run one of the following Scipion tests:

scipion test spider.tests.test_protocols_spider_reconstruct.TestSpiderReconstruct
scipion test spider.tests.test_protocols_spider_align.TestSpiderAlign
scipion test spider.tests.test_workflow_spiderMDA.TestSpiderWorkflow
scipion test spider.tests.test_workflow_spiderMDA.TestSpiderConvert
scipion test spider.tests.test_protocols_spider_projmatch.TestSpiderRefinement

A complete list of tests can also be seen by executing scipion test --show --grep spider

Supported versions

25.02

In 2018 the plugin was updated to support the latest (at that moment) SPIDER version - 25.02. This required a lot of code refactoring and the support of old SPIDER version 21.03 had to be discontinued. The full changelog since Scipion-1.x is available here.

Protocols

• Align AP SR

• Align pairwise

• CA PCA

• Classification protocols: Diday, K-means, Ward

• Custom 2D mask

• Filter particles

• Reconstruct Fourier

• Refinement

References

1. J. Frank et al. (1996). SPIDER and WEB: Processing and visualization of images in 3D electron microscopy and related fields. JSB. 116: 190-199.