Export

Convert merged reflection data (crystfel.hkl) into formats used by downstream software for structure solution and refinement.

Inputs

  • crystfel.hkl files produced by the Merge step (<stem>_merge_<timestamp>/merge-run<N>/crystfel.hkl)

  • Unit cell parameters (inferred automatically from the combined stream header)

Supported export formats

Format

Extension

Used by

HKLF4

.hkl

SHELX (SHELXL, SHELXT)

INS

.ins

SHELX instruction file for structure solution

P4P

.p4p

CrystalClear / Rigaku

MTZ

.mtz

CCP4 suite (REFMAC, Phaser, etc.)

Using the GUI

Open the Export window from the toolbar or menu. The window has three sections: Merge Runs, Cell, and Write files.

Merge Runs

Lists all crystfel.hkl files found under <stem>_merge_*/merge-run*/ in the workspace.

  • Refresh — rescan the workspace for HKL files.

  • Open Location — open the containing folder in the file browser.

Select an entry to populate the Cell section automatically.

Cell

Displays the unit cell parsed from the combined stream header. Point group is read from the merge settings JSON written alongside the stream.

Field

Editable

Source

Lattice type

after unlock

Stream header

Centering

after unlock

Stream header

Point group

read-only

Merge settings JSON

a, b, c (Å)

after unlock

Stream header

α, β, γ (°)

after unlock

Stream header

Space group

always

User entry

Composition

always

User entry

d_min (Å)

always

User entry

Click Enable edits… to unlock the lattice type, centering, and cell length/angle fields. Point group remains read-only.

  • Space group — required for MTZ export; also used by INS. Use standard notation (e.g. P 21 21 21).

  • Composition — chemical formula of the asymmetric unit used by INS (e.g. C6 H12 N2 O).

  • d_min (Å) — resolution cutoff applied during HKLF4 and MTZ export. Leave empty for no cutoff.

Write files

Control

Description

Export HKLF4

Write SHELX HKLF4 format.

Write INS

Generate a SHELX instruction file.

Write P4P

Generate a CrystalClear .p4p file.

Export MTZ

Convert to CCP4 MTZ format.

Anomalous

Keep Friedel pairs separate (applies to MTZ).

Overwrite existing files

Allow replacing output files that already exist.

All output files are written to the <stem>_merge_<timestamp>/ folder (the parent of the selected merge-run<N>/ directory).

Format-specific notes

HKLF4

Converts crystfel.hkl directly to SHELX HKLF4 format. Applies the d_min cutoff if set. The output is named <stem>.hkl.

INS

Generates a SHELX instruction file (<stem>.ins). Cell parameters, centering, and wavelength are taken from the parsed stream cell. Space group and composition are taken from the Cell section fields.

P4P

Generates a CrystalClear .p4p file (<stem>.p4p) from the unit cell. The non-centrosymmetric flag is inferred automatically from the point group read out of the merge settings.

MTZ

Converts crystfel.hkl to CCP4 MTZ format (<stem>.mtz). Requires:

  • Space group — must be filled in before export; COSEDA will not attempt a default.

  • Wavelength — parsed from the geometry block in the stream. If missing, the export is blocked until wavelength is entered manually via the Enable edits… flow.

  • Anomalous checkbox — controls whether Friedel pairs are kept separate.

  • d_min — optional resolution cutoff.

Polarisation is fixed to none for electron diffraction.

Outputs

All output files are placed in the <stem>_merge_<timestamp>/ folder next to the combined stream:

  • <stem>.hkl — HKLF4 reflection file

  • <stem>.ins — SHELX instruction file

  • <stem>.p4p — CrystalClear parameter file

  • <stem>.mtz — MTZ reflection file

Tips

  • Cell. COSEDA reads the unit cell from the combined stream’s header block. If parsing fails, click Enable edits… to enter values manually.

  • Wavelength. MTZ export requires a wavelength parsed from the geometry block embedded in the stream. If your stream does not contain one, unlock the cell fields and supply the value directly.

  • Multiple exports. Each format writes a separate output file; you can export to all four from the same HKL selection.

  • Overwrite. By default COSEDA refuses to overwrite existing output files. Tick Overwrite existing files before re-exporting with changed parameters.