Scaled unmerged data files - Revision history

Marcinw: correct filename from xdsme

2021-05-11T12:33:41Z

correct filename from xdsme

← Older revision		Revision as of 14:33, 11 May 2021
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	===xdsme===		===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)~~.		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>.

Marcinw: remove typo from the previous edit

2021-05-10T15:17:27Z

remove typo from the previous edit

← Older revision		Revision as of 17:17, 10 May 2021
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	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).		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~~===		===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>.

Marcinw: more details about xdsme

2021-05-10T15:16:09Z

more details about xdsme

← Older revision		Revision as of 17:16, 10 May 2021
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	===xdsme===		===xdsme===

	~~Since xdsme uses~~ XDS/~~XSCALE, see above~~.		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~~===		===x ia2===
	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>.

Marcinw: reword a sentence

2021-04-29T14:09:11Z

reword a sentence

← Older revision		Revision as of 16:09, 29 April 2021
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	Please ~~remember~~ that ~~a full deposition of~~ reflection data ~~will usually contain~~		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.

Kay: /* XDS / XSCALE */

2021-04-23T15:03:14Z

XDS / XSCALE

← Older revision		Revision as of 17:03, 23 April 2021
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	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].		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.

ClemensVonrhein: /* autoPROC */

2021-04-23T13:24:20Z

autoPROC

← Older revision		Revision as of 15:24, 23 April 2021
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	=== [https://www.globalphasing.com/autoproc/ 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 ~~processind~~ - and transfer the correct set of data quality metrics into the model mmCIF file.		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.		See also [https://www.globalphasing.com/buster/wiki/index.cgi?DepositionMmCif here] for more details.

ClemensVonrhein: /* Depositing */

2021-04-23T12:33:09Z

Depositing

← Older revision		Revision as of 14:33, 23 April 2021
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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 remember that a full deposition of reflection data will usually contain		Please remember that a full deposition of reflection data will usually contain
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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] ===
	~~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)~~.		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 processind - 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>.

	=== ~~StarANISO~~ ===		=== [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===		===XDS / XSCALE===

ClemensVonrhein: /* Depositing */

2021-04-23T11:33:26Z

Depositing

← Older revision		Revision as of 13:33, 23 April 2021
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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).
	An mmCIF with such data can be		A PDBx/mmCIF reflection data file with such data can be

	*generated by MX software suite (preferred way, ~~currently supported only by GPhL~~),		*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 ~~having around~~ a file with scaled unmerged data.		The prerequisite for the latter is a file with scaled unmerged data.

			Please remember that a full deposition of reflection data will usually contain
			* 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? ==

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

2021-04-22T17:43:31Z

autoPROC (autoBUSTER?): I meant autoPROC not autoBUSTER

← Older revision		Revision as of 19:43, 22 April 2021
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	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 ~~(autoBUSTER?)~~ ===		=== 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).		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).

Kay: /* Where to find scaled unmerged data? */ add autoPROC and put autoBUSTER in brackets because I don't think it applies

2021-04-22T17:11:14Z

Where to find scaled unmerged data?: add autoPROC and put autoBUSTER in brackets because I don't think it applies

← Older revision		Revision as of 19:11, 22 April 2021
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	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>.

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

	===CCP4i===		===CCP4i===