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wsmr-worked.md
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1 | +# Data Processing after WS-MR |
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2 | + |
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3 | +## 1 Verify Results for Search Models |
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4 | +The first follow-up step for a search model resulting from WSMR is to repeat MR locally. To download one of the search models; first click the "Load Top 100 Hits" button, click one of the yellow circles in the resulting plot, and then use the download link for the model. |
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5 | + |
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6 | +A typical input deck (`MR01.in` for this example) for `phaser` would look something like this (with the paths to your input `MTZ` and `PDB` files adjusted appropriately): |
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7 | + |
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8 | + ROOT MR01 |
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9 | + MODE MR_AUTO |
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10 | + HKLIn reflections.mtz |
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11 | + LABIn F=FP SIGF=SIGFP |
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12 | + ENSEmble SearchModel PDB model.pdb IDENtity 0.3 |
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13 | + COMPosition PERCENTAGE 0.50 |
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14 | + RESOlution HIGH 3.1 |
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15 | + SEARch ENSEmble SearchModel NUM 1 |
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16 | + SGALternative SELECT ALL |
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17 | + |
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18 | +This can be run with versions of `phaser` distributed with `CCP4` or `PHENIX` (with `phaser < MR01.in > MR01.out` or `phenix.phaser < MR01.in > MR01.out` respectively). The statistics (LLG and Z-scores) from local runs may differ due to differences in `phaser` versions. |
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19 | + |
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20 | +The `SGALternative` card is only necessary if you're checking alternative space-groups. |
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21 | + |
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22 | +## 2 Expand Search |
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23 | + |
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24 | +WSMR searches for a single copy of the search model - however there may be multiple copies of the model in the ASU. If so, the next step is the increase the `NUM` value for the `SEARch` card. When in doubt, it's better to set this too hight rather than too low - `phaser` will stop when unable to locate additional copies. |
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25 | + |
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26 | +## 3 Autobuild |
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27 | + |
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28 | +Once MR has been exhausted (no more copies of the search model can be placed), one possible next step is to use an autobuilder for an initial attempt to correct the sequence of the model. |
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29 | + |
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30 | +Using the `PHENIX` autobuilder: |
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31 | + |
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32 | +`phenix.autobuild reflections.mtz MR_Results.pdb project.fasta nproc=4 > AutoBuild01.out` |
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33 | + |
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34 | +The input model (`MR_Results.pdb`) for the autobuilder is the final result modeles from the initial or expanded MR search. |
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35 | + |
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36 | +The input `MTZ` file should be the original amplitudes (or intensities) used for searching, *not* the results from `phaser`. If phaser was run with the `SGALternative` card, make sure the spacegroup of this `MTZ` matches that of the search solutions. |
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37 | + |
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38 | +The `nproc=4` option should only be used if there are four (or more) available cores - when using the `rebuild_in_place` option, `phenix.autobuild` can't take advantage of more than 4 processors. |
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39 | + |