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examples/localrec_w_scipion.md
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1 | +## Local Reconstruction How To - Command line |
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2 | + |
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3 | +Refer to https://github.com/OPIC-Oxford/localrec/wiki/Using-the-Main-Script |
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4 | + |
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5 | +### Files required to start: |
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6 | +- Particles star file from a 3D refinement (containing angular information for each particle) |
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7 | +- Particle stacks |
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8 | +- Either know a vector to locate your feature of interest or use a Chimera Map Marker (CMM) file. |
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9 | +Instructions on this can be found here: https://github.com/OPIC-Oxford/localrec/wiki/Frequently-asked-questions |
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10 | + |
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11 | + |
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12 | +### Configuration changes required |
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13 | +- Ensure SBGrid environment is sourced |
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14 | +- Edit your scipion.conf file (located in ~/.config/scipion/scipion.conf) with your text editor of choice. |
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15 | +- 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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16 | +- Edit the RELION_HOME variable to “RELION_HOME = %(EM_ROOT)s/relion-1.4” and save the .conf file. |
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17 | + |
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18 | + |
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19 | +### Running locrec |
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20 | + |
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21 | +Run scripts from data processing directory for your data (ie. where you would launch your RELION GUI) |
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22 | +Run script with no arguments to get help text for running: “scipion run relion_localized_reconstruction.py” |
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23 | +Locrec script is run through scipion: |
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24 | + |
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25 | +``` |
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26 | +scipion run relion_localized_reconstruction.py --prepare_particles --create_subparticles --extract_subparticles --np 6 --sym I1 --vector \ |
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27 | + 0.382,0,1 --length 100 --angpix 1.35 --particle_size 480 --subparticle_size 100 --output example particles_data.star |
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28 | +``` |
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29 | + |
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30 | +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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31 | + |
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32 | +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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33 | + |
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34 | +You can then reconstruct a star model from these subparticles using: |
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35 | + |
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36 | +``` |
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37 | +scipion run relion_localized_reconstruction.py --reconstruct_subparticles --subsym C1 --maxres 15 --output example |
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38 | +``` |
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39 | + |
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40 | +Which can then be used as a starting model for 3D classifications of your subparticles within relion etc. |
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41 | + |
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42 | +**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.** |