Installing SBGrid Software
Using the SBGrid Environment
Support for Site Administrators
Hardware Support Notes
Getting Help
Support for Developers
Refer to https://github.com/OPIC-Oxford/localrec/wiki/Using-the-Main-Script
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.
This version of the page was edited by key at 2018-05-25 17:22:19. View the most recent version.