examples/localrec_w_scipion.md
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+## Local Reconstruction How To - Command line
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+
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+Refer to https://github.com/OPIC-Oxford/localrec/wiki/Using-the-Main-Script
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+
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+### Files required to start:
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+- Particles star file from a 3D refinement (containing angular information for each particle)
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+- Particle stacks
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+- Either know a vector to locate your feature of interest or use a Chimera Map Marker (CMM) file.
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+Instructions on this can be found here: https://github.com/OPIC-Oxford/localrec/wiki/Frequently-asked-questions
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+
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+
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+### Configuration changes required
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+- Ensure SBGrid environment is sourced
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+- Edit your scipion.conf file (located in ~/.config/scipion/scipion.conf) with your text editor of choice.
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+- 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.
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+- Edit the RELION_HOME variable to “RELION_HOME = %(EM_ROOT)s/relion-1.4” and save the .conf file.
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+
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+
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+### Running locrec
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+
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+Run scripts from data processing directory for your data (ie. where you would launch your RELION GUI)
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+Run script with no arguments to get help text for running: “scipion run relion_localized_reconstruction.py”
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+Locrec script is run through scipion:
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+
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+```
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+scipion run relion_localized_reconstruction.py --prepare_particles --create_subparticles --extract_subparticles --np 6 --sym I1 --vector \
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+ 0.382,0,1 --length 100 --angpix 1.35 --particle_size 480 --subparticle_size 100 --output example particles_data.star
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+```
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+
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+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
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+To perform signal subtraction you also need the *--masked_map* option using a prepared model as described in the original signal subtraction publications.
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+You can then reconstruct a star model from these subparticles using:
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+
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+```
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+scipion run relion_localized_reconstruction.py --reconstruct_subparticles --subsym C1 --maxres 15 --output example
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+```
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+
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+Which can then be used as a starting model for 3D classifications of your subparticles within relion etc.
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+**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.**