# 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.