localrec_w_scipion

Local Reconstruction How To

Configuration changes are required in SCIPION to run local reconstruction. This page outlines those changes and command line instructions.

Refer to https://github.com/OPIC-Oxford/localrec/wiki/Using-the-Main-Script

Files required to start:

• Particles star file from a 3D refinement (containing angular information for each particle)
• Particle stacks
• Either know a vector to locate your feature of interest or use a Chimera Map Marker (CMM) file. Instructions on this can be found here: https://github.com/OPIC-Oxford/localrec/wiki/Frequently-asked-questions

Configuration changes required

• Ensure SBGrid environment is sourced
• Edit your scipion.conf file (located in ~/.config/scipion/scipion.conf) with your text editor of choice.
• If the ~/.config/scipion/scipion.conf file does not exist first run scipion GUI using the command “scipion” and follow the on screen instructions which should create the file.
• Edit the RELION_HOME variable to “RELION_HOME = %(EM_ROOT)s/relion-1.4” and save the .conf file.

Running locrec

Run scripts from data processing directory for your data (ie. where you would launch your RELION GUI) Run script with no arguments to get help text for running: “scipion run relion_localized_reconstruction.py” Locrec script is run through scipion:

scipion run relion_localized_reconstruction.py --prepare_particles --create_subparticles --extract_subparticles --np 6 --sym I1 --vector \
 0.382,0,1 --length 100 --angpix 1.35 --particle_size 480 --subparticle_size 100 --output example particles_data.star

With all 3 --prepare_particles --create_subparticles --extract_subparticles arguments this will leave you with extracted subparticles in your output folder and a new star file called example.star in this case

To perform signal subtraction you also need the --masked_map option using a prepared model as described in the original signal subtraction publications.

You can then reconstruct a star model from these subparticles using:

scipion run relion_localized_reconstruction.py --reconstruct_subparticles --subsym C1 --maxres 15 --output example

Which can then be used as a starting model for 3D classifications of your subparticles within relion etc.

If you intend on using Scipion for anything else (classification/refinement etc.) remember to edit the RELION_HOME variable in your .conf file so that it again uses the correct relion2.1 version.