CCP4 wiki - User contributions [en]

Scaled unmerged data files

2021-05-11T12:33:41Z

Marcinw: correct filename from xdsme

== Depositing ==
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]
announced in 2021).
A PDBx/mmCIF reflection data file with such data can be

*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 [https://github.com/project-gemmi/gemmi GEMMI].

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? ==

===[http://legacy.ccp4.ac.uk/html/aimless.html Aimless]===
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===
i1 has a few tasks that scale data:

* Scale and Merge Intensities – it uses obsolete SCALA program. To write scaled unmerged data check <code>☑ Customize Scala process</code> and select Output <code>scaled unmerged & no outliers</code> (?).
* Symmetry, Scale, Merge (Aimless) – check <code>☑ Customize output options</code> and select MTZ Output <code>both merged and unmerged</code>.
* Find Symmetry, Scale & Merge (Scala) – obsolete, use Aimless instead.

===CCP4i2===
To store scaled unmerged data in ''Data reduction - AIMLESS'' task you need to open Important Options and check:

☑ ''output unmerged data as well as merged''

===CCP4 Cloud===
Saving scaled unmerged data is not supported?

===dials.scale===
To output scaled unmerged MTZ file either add option unmerged_mtz=FILE:

<code>dials.scale symmetrized.expt symmetrized.refl unmerged_mtz=scaled_unmerged.mtz</code>

or use dials.export afterwards:

<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===

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 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 scaled unmerged data in the SCALEPACK format.

===SCALA===
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].

===[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.

===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===
Scaled unmerged MTZ file is stored as <code>DataFiles/*_scaled_unmerged.mtz</code>.

Scaled unmerged data files

2021-05-10T15:17:27Z

Marcinw: remove typo from the previous edit

== Depositing ==
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]
announced in 2021).
A PDBx/mmCIF reflection data file with such data can be

*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 [https://github.com/project-gemmi/gemmi GEMMI].

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? ==

===[http://legacy.ccp4.ac.uk/html/aimless.html Aimless]===
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===
i1 has a few tasks that scale data:

* Scale and Merge Intensities – it uses obsolete SCALA program. To write scaled unmerged data check <code>☑ Customize Scala process</code> and select Output <code>scaled unmerged & no outliers</code> (?).
* Symmetry, Scale, Merge (Aimless) – check <code>☑ Customize output options</code> and select MTZ Output <code>both merged and unmerged</code>.
* Find Symmetry, Scale & Merge (Scala) – obsolete, use Aimless instead.

===CCP4i2===
To store scaled unmerged data in ''Data reduction - AIMLESS'' task you need to open Important Options and check:

☑ ''output unmerged data as well as merged''

===CCP4 Cloud===
Saving scaled unmerged data is not supported?

===dials.scale===
To output scaled unmerged MTZ file either add option unmerged_mtz=FILE:

<code>dials.scale symmetrized.expt symmetrized.refl unmerged_mtz=scaled_unmerged.mtz</code>

or use dials.export afterwards:

<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===

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 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 scaled unmerged data in the SCALEPACK format.

===SCALA===
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].

===[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.

===xdsme===

Uses XDS and outputs scaled unmerged <code>XDS_ASCII.HKL</code> and <code>*_aimless.mtz</code>. The latter is converted from the former using Aimless (without rescaling).

===xia2===
Scaled unmerged MTZ file is stored as <code>DataFiles/*_scaled_unmerged.mtz</code>.

Scaled unmerged data files

2021-05-10T15:16:09Z

Marcinw: more details about xdsme

== Depositing ==
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]
announced in 2021).
A PDBx/mmCIF reflection data file with such data can be

*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 [https://github.com/project-gemmi/gemmi GEMMI].

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? ==

===[http://legacy.ccp4.ac.uk/html/aimless.html Aimless]===
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===
i1 has a few tasks that scale data:

* Scale and Merge Intensities – it uses obsolete SCALA program. To write scaled unmerged data check <code>☑ Customize Scala process</code> and select Output <code>scaled unmerged & no outliers</code> (?).
* Symmetry, Scale, Merge (Aimless) – check <code>☑ Customize output options</code> and select MTZ Output <code>both merged and unmerged</code>.
* Find Symmetry, Scale & Merge (Scala) – obsolete, use Aimless instead.

===CCP4i2===
To store scaled unmerged data in ''Data reduction - AIMLESS'' task you need to open Important Options and check:

☑ ''output unmerged data as well as merged''

===CCP4 Cloud===
Saving scaled unmerged data is not supported?

===dials.scale===
To output scaled unmerged MTZ file either add option unmerged_mtz=FILE:

<code>dials.scale symmetrized.expt symmetrized.refl unmerged_mtz=scaled_unmerged.mtz</code>

or use dials.export afterwards:

<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===

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 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 scaled unmerged data in the SCALEPACK format.

===SCALA===
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].

===[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.

===xdsme===

Uses XDS and outputs scaled unmerged <code>XDS_ASCII.HKL</code> and <code>*_aimless.mtz</code>. The latter is converted from the former using Aimless (without rescaling).

===x ia2===
Scaled unmerged MTZ file is stored as <code>DataFiles/*_scaled_unmerged.mtz</code>.

Scaled unmerged data files

2021-04-29T14:09:11Z

Marcinw: reword a sentence

== Depositing ==
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]
announced in 2021).
A PDBx/mmCIF reflection data file with such data can be

*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 [https://github.com/project-gemmi/gemmi GEMMI].

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? ==

===[http://legacy.ccp4.ac.uk/html/aimless.html Aimless]===
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===
i1 has a few tasks that scale data:

* Scale and Merge Intensities – it uses obsolete SCALA program. To write scaled unmerged data check <code>☑ Customize Scala process</code> and select Output <code>scaled unmerged & no outliers</code> (?).
* Symmetry, Scale, Merge (Aimless) – check <code>☑ Customize output options</code> and select MTZ Output <code>both merged and unmerged</code>.
* Find Symmetry, Scale & Merge (Scala) – obsolete, use Aimless instead.

===CCP4i2===
To store scaled unmerged data in ''Data reduction - AIMLESS'' task you need to open Important Options and check:

☑ ''output unmerged data as well as merged''

===CCP4 Cloud===
Saving scaled unmerged data is not supported?

===dials.scale===
To output scaled unmerged MTZ file either add option unmerged_mtz=FILE:

<code>dials.scale symmetrized.expt symmetrized.refl unmerged_mtz=scaled_unmerged.mtz</code>

or use dials.export afterwards:

<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===

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 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 scaled unmerged data in the SCALEPACK format.

===SCALA===
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].

===[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.

===xdsme===

Since xdsme uses XDS/XSCALE, see above.

===xia2===
Scaled unmerged MTZ file is stored as <code>DataFiles/*_scaled_unmerged.mtz</code>.

Scaled unmerged data files

2021-04-22T17:43:31Z

Marcinw: /* autoPROC (autoBUSTER?) */ I meant autoPROC not autoBUSTER

== Depositing ==
A deposition to the wwPDB may include 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]
announced in 2021).
An mmCIF with such data can be

*generated by MX software suite (preferred way, currently supported only by GPhL),
*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.

The prerequisite for the latter is having around a file with scaled unmerged data.

== Where to find scaled unmerged data? ==

===Aimless===
If you run Aimless from the command-line add option <code>OUTPUT MTZ UNMERGED</code>.

=== autoPROC ===
Scaled unmerged data is stored in <code>scaled.mtz</code> as well as in mmCIF file (GPhL developers recommend to use the mmCIF file and <code>aB_deposition_combine</code> to prepare files for deposition).

===CCP4i===
i1 has a few tasks that scale data:

* Scale and Merge Intensities – it uses obsolete SCALA program. To write scaled unmerged data check <code>☑ Customize Scala process</code> and select Output <code>scaled unmerged & no outliers</code> (?).
* Symmetry, Scale, Merge (Aimless) – check <code>☑ Customize output options</code> and select MTZ Output <code>both merged and unmerged</code>.
* Find Symmetry, Scale & Merge (Scala) – obsolete, use Aimless instead.

===CCP4i2===
To store scaled unmerged data in ''Data reduction - AIMLESS'' task you need to open Important Options and check:

☑ ''output unmerged data as well as merged''

===CCP4 Cloud===
Saving scaled unmerged data is not supported?

===dials.scale===
To output scaled unmerged MTZ file either add option unmerged_mtz=FILE:

<code>dials.scale symmetrized.expt symmetrized.refl unmerged_mtz=scaled_unmerged.mtz</code>

or use dials.export afterwards:

<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===

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 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 scaled unmerged data in the SCALEPACK format.

===SCALA===
CCP4 SCALA program got obsoleted in favor of Aimless. It has option <code>OUTPUT UNMERGED</code>.

=== StarANISO ===
?

===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.

===xdsme===

Since xdsme uses XDS/XSCALE, see above.

===xia2===
Scaled unmerged MTZ file is stored as <code>DataFiles/*_scaled_unmerged.mtz</code>.

Scaled unmerged data files

2021-04-22T15:25:19Z

Marcinw: add DUI

== Depositing ==
A deposition to the wwPDB may include 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]
announced in 2021).
An mmCIF with such data can be

*generated by MX software suite (preferred way, currently supported only by GPhL),
*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.

The prerequisite for the latter is having around a file with scaled unmerged data.

== Where to find scaled unmerged data? ==

===Aimless===
If you run Aimless from the command-line add option <code>OUTPUT MTZ UNMERGED</code>.

===autoBUSTER===
Scaled unmerged data is stored in <code>scaled.mtz</code> as well as in mmCIF file
(GPhL developers recommend to use the mmCIF file and <code>aB_deposition_combine</code> to prepare files for deposition).

===CCP4i===
i1 has a few tasks that scale data:

* Scale and Merge Intensities – it uses obsolete SCALA program. To write scaled unmerged data check <code>☑ Customize Scala process</code> and select Output <code>scaled unmerged & no outliers</code> (?).
* Symmetry, Scale, Merge (Aimless) – check <code>☑ Customize output options</code> and select MTZ Output <code>both merged and unmerged</code>.
* Find Symmetry, Scale & Merge (Scala) – obsolete, use Aimless instead.

===CCP4i2===
To store scaled unmerged data in ''Data reduction - AIMLESS'' task you need to open Important Options and check:

☑ ''output unmerged data as well as merged''

===CCP4 Cloud===
Saving scaled unmerged data is not supported?

===dials.scale===
To output scaled unmerged MTZ file either add option unmerged_mtz=FILE:

<code>dials.scale symmetrized.expt symmetrized.refl unmerged_mtz=scaled_unmerged.mtz</code>

or use dials.export afterwards:

<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===
?

===iMosflm===
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 scaled unmerged data in the SCALEPACK format.

===SCALA===
CCP4 SCALA program got obsoleted in favor of Aimless. It has option <code>OUTPUT UNMERGED</code>.

===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.

===xdsme===
?

===xia2===
Scaled unmerged MTZ file is stored as <code>DataFiles/*_scaled_unmerged.mtz</code>.

Scaled unmerged data files

2021-04-22T13:42:08Z

Marcinw: edit headers

== Depositing ==
A deposition to the wwPDB may include 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]
announced in 2021).
An mmCIF with such data can be

*generated by MX software suite (preferred way, currently supported only by GPhL),
*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.

The prerequisite for the latter is having around a file with scaled unmerged data.

== Where to find scaled unmerged data? ==

===Aimless===
If you run Aimless from the command-line add option <code>OUTPUT MTZ UNMERGED</code>.

===autoBUSTER===
Scaled unmerged data is stored in <code>scaled.mtz</code> as well as in mmCIF file
(GPhL developers recommend to use the mmCIF file and <code>aB_deposition_combine</code> to prepare files for deposition).

===CCP4i===
i1 has a few tasks that scale data:

* Scale and Merge Intensities – it uses obsolete SCALA program. To write scaled unmerged data check <code>☑ Customize Scala process</code> and select Output <code>scaled unmerged & no outliers</code> (?).
* Symmetry, Scale, Merge (Aimless) – check <code>☑ Customize output options</code> and select MTZ Output <code>both merged and unmerged</code>.
* Find Symmetry, Scale & Merge (Scala) – obsolete, use Aimless instead.

===CCP4i2===
To store scaled unmerged data in ''Data reduction - AIMLESS'' task you need to open Important Options and check:

☑ ''output unmerged data as well as merged''

===CCP4 Cloud===
?

===dials.scale===
To output scaled unmerged MTZ file either add option unmerged_mtz=FILE:

<code>dials.scale symmetrized.expt symmetrized.refl unmerged_mtz=scaled_unmerged.mtz</code>

or use dials.export afterwards:

<code>dials.export scaled.refl scaled.expt</code>

===HKL2000===
?

===iMosflm===
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.

===SCALA===
CCP4 SCALA program got obsoleted in favor of Aimless. It has option <code>OUTPUT UNMERGED</code>.

===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.

===xdsme===
?

===xia2===
Scaled unmerged MTZ file is stored as <code>DataFiles/*_scaled_unmerged.mtz</code>.

Scaled unmerged data files

2021-04-22T13:28:08Z

Marcinw: /* dials.scale */

=Where to find scaled unmerged data?=
A deposition to the wwPDB may include 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]
announced in 2021).
An mmCIF with such data can be

*generated by MX software suite (preferred, but currently only supported by GPhL),
*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.

The prerequisite for the latter is having around a file with scaled unmerged data.
This page describes how to create such a file in MX programs, pipelines and GUIs.

===Aimless===
If you run Aimless from the command-line add option <code>OUTPUT MTZ UNMERGED</code>.

===autoBUSTER===
Scaled unmerged data is stored in <code>scaled.mtz</code> as well as in mmCIF file
(GPhL developers recommend to use the mmCIF file and <code>aB_deposition_combine</code> to prepare files for deposition).

===CCP4i===
It has a few tasks that scale data:

* Scale and Merge Intensities – it uses obsolete SCALA program. To write scaled unmerged data check <code>☑ Customize Scala process</code> and select Output <code>scaled unmerged & no outliers</code> (?).
* Symmetry, Scale, Merge (Aimless) – check <code>☑ Customize output options</code> and select MTZ Output <code>both merged and unmerged</code>.
* Find Symmetry, Scale & Merge (Scala) – obsolete, use Aimless instead

===CCP4i2===
To store scaled unmerged data in ''Data reduction - AIMLESS'' task you need to open Important Options and check:

☑ ''output unmerged data as well as merged''

===CCP4 Cloud===
?

===dials.scale===
To output scaled unmerged MTZ file either add option unmerged_mtz=FILE:

<code>dials.scale symmetrized.expt symmetrized.refl unmerged_mtz=scaled_unmerged.mtz</code>

or use dials.export afterwards:

<code>dials.export scaled.refl scaled.expt</code>

===HKL2000===
?

===iMosflm===
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.

===SCALA===
CCP4 SCALA program got obsoleted in favor of Aimless. It has option <code>OUTPUT UNMERGED</code>.

===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.

===xdsme===
?

===xia2===
Scaled unmerged MTZ file is stored as <code>DataFiles/*_scaled_unmerged.mtz</code>.

Scaled unmerged data files

2021-04-22T11:57:49Z

Marcinw: edited section about CCP4i and some others

=Where to find scaled unmerged data?=
A deposition to the wwPDB may include 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]
announced in 2021).
An mmCIF with such data can be

*generated by MX software suite (preferred, but currently only supported by GPhL),
*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.

The prerequisite for the latter is having around a file with scaled unmerged data.
This page describes how to create such a file in MX programs, pipelines and GUIs.

===Aimless===
If you run Aimless from the command-line add option <code>OUTPUT MTZ UNMERGED</code>.

===autoBUSTER===
Scaled unmerged data is stored in <code>scaled.mtz</code> as well as in mmCIF file
(GPhL developers recommend to use the mmCIF file and <code>aB_deposition_combine</code> to prepare files for deposition).

===CCP4i===
It has a few tasks that scale data:

* Scale and Merge Intensities – it uses obsolete SCALA program. To write scaled unmerged data check <code>☑ Customize Scala process</code> and select Output <code>scaled unmerged & no outliers</code> (?).
* Symmetry, Scale, Merge (Aimless) – check <code>☑ Customize output options</code> and select MTZ Output <code>both merged and unmerged</code>.
* Find Symmetry, Scale & Merge (Scala) – obsolete, use Aimless instead

===CCP4i2===
To store scaled unmerged data in ''Data reduction - AIMLESS'' task you need to open Important Options and check:

☑ ''output unmerged data as well as merged''

===CCP4 Cloud===
?

===dials.scale===
?

===HKL2000===
?

===iMosflm===
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.

===SCALA===
CCP4 SCALA program got obsoleted in favor of Aimless. It has option <code>OUTPUT UNMERGED</code>.

===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.

===xdsme===
?

===xia2===
Scaled unmerged MTZ file is stored as <code>DataFiles/*_scaled_unmerged.mtz</code>.

Scaled unmerged data files

2021-04-22T11:28:14Z

Marcinw: added CCP4 Cloud

=Where to find scaled unmerged data?=
A deposition to the wwPDB may include 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]
announced in 2021).
An mmCIF with such data can be

*generated by MX software suite (preferred, but currently only supported by GPhL),
*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.

The prerequisite for the latter is having around a file with scaled unmerged data.
This page describes how to create such a file in MX programs, pipelines and GUIs.

===Aimless===
If you run Aimless from the command-line add option <code>OUTPUT MTZ UNMERGED</code>.

===autoBUSTER===
Scaled unmerged data is stored in <code>scaled.mtz</code> as well as in mmCIF file
(GPhL developers recommend to use the mmCIF file and <code>aB_deposition_combine</code> to prepare files for deposition).

===CCP4i===
?

===CCP4i2===
To store scaled unmerged data in ''Data reduction - AIMLESS'' task you need to open Important Options and check:

☑ ''output unmerged data as well as merged''

===CCP4 Cloud===
?

===dials.scale===
to be written

===HKL2000===
?

===iMosflm===
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.

===SCALA===
CCP4 SCALA program got obsoleted in favor of Aimless (scaling program written by the same author).

===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.

===xdsme===
?

===xia2===
Scaled unmerged MTZ file is stored as <code>DataFiles/*_scaled_unmerged.mtz</code>.

Scaled unmerged data files

2021-04-22T11:26:18Z

Marcinw: created page on finding scaled unmerged data

=Where to find scaled unmerged data?=
A deposition to the wwPDB may include 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]
announced in 2021).
An mmCIF with such data can be

*generated by MX software suite (preferred, but currently only supported by GPhL),
*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.

The prerequisite for the latter is having around a file with scaled unmerged data.
This page describes how to create such a file in MX programs, pipelines and GUIs.

===Aimless===
If you run Aimless from the command-line add option <code>OUTPUT MTZ UNMERGED</code>.

===autoBUSTER===
Scaled unmerged data is stored in <code>scaled.mtz</code> as well as in mmCIF file
(GPhL developers recommend to use the mmCIF file and <code>aB_deposition_combine</code> to prepare files for deposition).

===CCP4i===
?

===CCP4i2===
To store scaled unmerged data in ''Data reduction - AIMLESS'' task you need to open Important Options and check:

☑ ''output unmerged data as well as merged''

===dials.scale===
to be written

===HKL2000===
?

===iMosflm===
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.

===SCALA===
CCP4 SCALA program got obsoleted in favor of Aimless (scaling program written by the same author).

===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.

===xdsme===
?

===xia2===
Scaled unmerged MTZ file is stored as <code>DataFiles/*_scaled_unmerged.mtz</code>.