Using RELION data in SPIDER

A guide for importing RELION's classification or refinement data into SPIDER

If you have run a RELION classification or refinement of your data and desire to import the data into SPIDER the following steps are advised.

1. Create and access Reconstruction directory. Fill directory with particle data. If these particles are not in SPIDER format they should be converted to SPIDER stack format (e.g. use: 'CP FROM MRC' and should keep the names used in Relion.

   ¤	mkdir -p Alignment/input   Reconstruction	Create & access directories
   ¤	cp myproject/Relion/input/data*.spi   Alignment/input	Access unaligned, windowed SPIDER stacks of particle data

2. Ensure that particle images have been CTF corrected by phase flipping.

   In order to avoid grouping the particle images by defocus level the images have to be CTF corrected by phase flipping before following the protocol given in: Reconstruction Using Projection Matching, Without Defocus Groups. The CTF correction may have been done within RELION pre-processing, in which case you can skip to the next step. If not, use SPIDER as follows:

   You probably have already used make-ctf-cor.spi to create the necessary doc files of the background-subtracted one-dimensional power spectra and a doc file containing defocus values for each micrograph. If not, you must do so at this time.

   These doc files are then used as input to CTF correct the particle images using phase flipping and assign them to groups for parallelization. The number of new groups is arbitrary, but a reasonable choice would be the number of nodes available on your compute cluster. If subsequent alignment is not going to be parallelized, the number of new groups can be set to 1. Use restack-n-ctf.spi following the protocol in: Reconstruction Using Projection Matching, Without Defocus Groups.

   That procedure creates:

   ¤	sel_group:	New group selection doc file.
   ¤	data_ctf_***:	New CTF corrected particle image stacks.
   ¤	sel_part_***:	New particle selection doc files.
   ¤	part2glonum_***:	Lookup tables listing global number for particles.

3. Convert Relion's star data file to a set of SPIDER document files.

   The conversion procedure relion_star_to_align.spi uses SPIDER operation 'XM S2D': :

   • Converts Relion's alignment parameters for projection direction, shifts & rotation to SPIDER's convention, and puts them in a SPIDER alignment parameter file.
   • Extracts one/two numerals from the Relion file names as necessary.
   • Creates a new group selection file listing any groups extracted from Relion's file names.
   • Creates new group particle selection files listing particle numbers extracted from Relion's file names.

   It reads a Star iteration data file (e.g. classify_it010_data.star) and creates:

   ¤	sel_grp	Group selection file.
   ¤	sel_part_***:	Particle selection doc files.
   ¤	ali_doc_***:	Group alignment files.

   Usage:

   ¤	cd Reconstruction	Access Reconstruction directory.
   ¤	cp relion_star_to_align.spi .	Load star file conversion procedure.
   ¤	edit relion_star_to_align.spi	Edit file names as needed
   ¤	spider spi/dat @relion_star_to_align	Run conversion procedure in SPIDER.

4. Continue with reconstruction in the Reconstruction directory as desired.

   Note that reconstruction using SPIDER from Relion's alignment parameters is not expected to give a reconstruction of the same resolution as the Relion reconstructions. The alignment parameters reported by Relion are only for the optimal alignment of the projected particle and do not use maximum likelihood's summation of fuzzy alignments.

   .

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Source: relion2spi.html     Page updated: Apr. 29 2014     ArDean Leith