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Scaled unmerged data files: Difference between revisions
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correct filename from xdsme
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The prerequisite for the latter is a file with scaled unmerged data. | The prerequisite for the latter is a file with scaled unmerged data. | ||
Please | |||
Please note that autoPROC+BUSTER outputs reflection data mmCIF that contains | |||
* The data that went into the final refinement step (to provide the possibility for validation and re-refinement) | * The data that went into the final refinement step (to provide the possibility for validation and re-refinement) | ||
* The output of the refinement program - including map coefficients for the 2mFo-DFc (electron) density map and the mFo-DFc difference density map. This will allow a user to compute the maps exactly as seen by the depositor, i.e. those maps any original model interpretation were based upon. | * The output of the refinement program - including map coefficients for the 2mFo-DFc (electron) density map and the mFo-DFc difference density map. This will allow a user to compute the maps exactly as seen by the depositor, i.e. those maps any original model interpretation were based upon. | ||
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== Where to find scaled unmerged data? == | == Where to find scaled unmerged data? == | ||
===Aimless=== | ===[http://legacy.ccp4.ac.uk/html/aimless.html Aimless]=== | ||
If you run Aimless from the command-line add option <code>OUTPUT MTZ UNMERGED</code>. | If you run Aimless from the command-line add option <code>OUTPUT MTZ UNMERGED</code>. | ||
=== autoPROC === | === [https://www.globalphasing.com/autoproc/ autoPROC] === | ||
Individual scaled unmerged data is stored in <code>*unmerged.mtz</code>. However, full deposition-ready PDBx/mmCIF files are already generated (including multiple datablocks with merged and unmerged data) - including the full set of data quality metrics: <code>Data_1_autoPROC_STARANISO_all.cif</code> (for the anisotropic/STARANISO analysed data) and <code>Data_2_autoPROC_TRUNCATE_all.cif</code> (for the traditional/isotropic data). These can be used as-is for deposition and no subsequent format conversion from MTZ is required. Furthermore, no additional extraction of data quality metrics should be necessary. If [https://www.globalphasing.com/buster/ BUSTER] was used for structure refinement, the <code>aB_deposition_combine</code> tool can be used to combine the reflection mmCIF file from refinement with this one from data processing - and transfer the correct set of data quality metrics into the model mmCIF file. | |||
See also [https://www.globalphasing.com/buster/wiki/index.cgi?DepositionMmCif here] for more details. | |||
===CCP4i=== | ===CCP4i=== | ||
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CCP4 SCALA program got obsoleted in favor of Aimless. It has option <code>OUTPUT UNMERGED</code>. | CCP4 SCALA program got obsoleted in favor of Aimless. It has option <code>OUTPUT UNMERGED</code>. | ||
=== | === [https://staraniso.globalphasing.org STARANISO] === | ||
See [https://staraniso.globalphasing.org/deposition_about.html here] for up-to-date details regarding deposition and mmCIF files generated already on the [https://staraniso.globalphasing.org STARANISO server]. | |||
===XDS / XSCALE=== | ===[http://xds.mpimf-heidelberg.mpg.de XDS / XSCALE]=== | ||
Scaled unmerged data from XDS CORRECT and XSCALE is written in the XDS_ASCII.HKL format. The GEMMI converter can use these files directly. | Scaled unmerged data from XDS CORRECT and XSCALE is written in the XDS_ASCII.HKL format. The GEMMI converter can use these files directly. | ||
===xdsme=== | ===xdsme=== | ||
Uses XDS and outputs scaled unmerged <code>XDS_ASCII.HKL</code> and <code>{image-glob}_pointless.mtz</code>. The latter is converted from the former using Pointless. | |||
===xia2=== | ===xia2=== | ||
Scaled unmerged MTZ file is stored as <code>DataFiles/*_scaled_unmerged.mtz</code>. | Scaled unmerged MTZ file is stored as <code>DataFiles/*_scaled_unmerged.mtz</code>. | ||