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Scaled unmerged data files: Difference between revisions
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== Depositing == | == Depositing == | ||
A deposition to the wwPDB may include scaled unmerged data (as part of the | A deposition to the wwPDB may not only include merged reflection data (i.e. the typical input to the refinement program), but also scaled unmerged data (as part of the | ||
[https://www.wwpdb.org/news/news?year=2021#60638da1931d5660393084c3 Improved support for extended PDBx/mmCIF structure factor files] | [https://www.wwpdb.org/news/news?year=2021#60638da1931d5660393084c3 Improved support for extended PDBx/mmCIF structure factor files] | ||
announced in 2021). | announced in 2021). | ||
A PDBx/mmCIF reflection data file with such data can be | |||
*generated by MX software suite (preferred way, | *generated by a MX software suite directly (which is often the preferred way, since it will typically also contain the data quality metrics describing the data) - see e.g. [https://www.globalphasing.com/autoproc/ autoPROC] from [https://www.globalphasnig.com/ Global Phasing], | ||
*generated by [https://project-gemmi.github.io/wasm/mxdepo.html this web app] or the equivalent command-line program, both developed as part of project GEMMI. | *generated by [https://project-gemmi.github.io/wasm/mxdepo.html this web app] or the equivalent command-line program, both developed as part of project [https://github.com/project-gemmi/gemmi GEMMI]. | ||
The prerequisite for the latter is | The prerequisite for the latter is a file with scaled unmerged data. | ||
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 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. | |||
* (optionally) the scaled and merged data before a final step of data selection, application of a cut-off or re-scaling. | |||
* The scaled and unmerged data discussed on this page. | |||
* (optionally) Additional reflection data that describe for example subsets of the data, different wavelengths or such. | |||
* A set of data quality metrics for each of those separate reflection datablocks (R-values, completeness, redundancy, CC1/2, mean I/sig(I) etc). | |||
== 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>. | ||
=== | === [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 Cloud=== | ===CCP4 Cloud=== | ||
? | Saving scaled unmerged data is not supported? | ||
===dials.scale=== | ===dials.scale=== | ||
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<code>dials.export scaled.refl scaled.expt</code> | <code>dials.export scaled.refl scaled.expt</code> | ||
===DUI=== | |||
The DIALS User Interface has 8 steps. The last one is ''export'' which writes unmerged MTZ file. The option ''Output Scaled Intensities'' must be checked (default) to write scaled unmerged data. | |||
===HKL2000=== | ===HKL2000=== | ||
The 'no merge original index' macro for SCALEPACK produces a non-standard .sca file. It cannot be used, for example, for structure solution in HKL2000, and therefore gives a warning. | |||
===iMosflm=== | ===iMosflm=== | ||
iMosflm can scale data with Aimless. Scaled unmerged MTZ file is written by default since v7.4.0 (soon to be released). | iMosflm can scale data with Aimless. Scaled unmerged MTZ file is written by default since v7.4.0 (soon to be released). | ||
Older versions had option (off by default) to write data in the SCALEPACK format. | Older versions had option (off by default) to write scaled unmerged data in the SCALEPACK format. | ||
===SCALA=== | ===SCALA=== | ||
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>. | ||
===XDS / XSCALE=== | === [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]. | |||
===[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>. | ||