Scaled unmerged data files: Difference between revisions
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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=== | ||
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===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=== | ||
Revision as of 16:25, 22 April 2021
Depositing
A deposition to the wwPDB may include scaled unmerged data (as part of the 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 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 OUTPUT MTZ UNMERGED.
autoBUSTER
Scaled unmerged data is stored in scaled.mtz as well as in mmCIF file
(GPhL developers recommend to use the mmCIF file and aB_deposition_combine 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
☑ Customize Scala processand select Outputscaled unmerged & no outliers(?). - Symmetry, Scale, Merge (Aimless) – check
☑ Customize output optionsand select MTZ Outputboth merged and unmerged. - 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:
dials.scale symmetrized.expt symmetrized.refl unmerged_mtz=scaled_unmerged.mtz
or use dials.export afterwards:
dials.export scaled.refl scaled.expt
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 OUTPUT UNMERGED.
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 DataFiles/*_scaled_unmerged.mtz.