scipion-em-spider 3.1.1

Plugin to use Spider programs within the Scipion framework

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

prod:

devel:

support:

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-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.