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add xlms-tools info #28

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Feb 5, 2024
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add xlms-tools info #28

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add xlms-tools
michabirklbauer Feb 5, 2024
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michabirklbauer Feb 5, 2024
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7 changes: 7 additions & 0 deletions README.md
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Expand Up @@ -47,6 +47,8 @@ Results can then be exported by selecting `File > Export > To Microsoft Excel…
```
python pyXlinkViewerExporter_msannika.py result.xlsx -pdb structure.pdb
```
- **Exporting to XLMS-Tools**
XLMS-Tools uses the same file format as pyXlinkViewer, therefore the same exporter can be used!
- **Exporting to XMAS (ChimeraX)**
Visualization of MS Annika results works out of the box with .xlsx files exported from Proteome Discoverer.
- **Exporting to PAE Viewer**
Expand Down Expand Up @@ -202,6 +204,11 @@ Or using the Windows binary:
pyXlinkViewerExporter_msannika.exe "202001216_nsp8_trypsin_XL_REP1.xlsx" "202001216_nsp8_trypsin_XL_REP2.xlsx" "202001216_nsp8_trypsin_XL_REP3.xlsx" --pdb 6yhu.pdb -o test
```

## Export to [XLMS-Tools](https://gitlab.com/topf-lab/xlms-tools)

[XLMS-Tools](https://gitlab.com/topf-lab/xlms-tools) uses the same input format as [pyXlinkViewer](https://github.com/BobSchiffrin/PyXlinkViewer).
Please use the [pyXlinkViewer exporter](#export-to-pyxlinkviewer-for-pymol) to export your results to XLMS-Tools format.

## Export to [XMAS for ChimeraX](https://github.com/ScheltemaLab/ChimeraX_bundle)

Visualization of crosslinks with [XMAS](https://github.com/ScheltemaLab/ChimeraX_bundle) in ChimeraX works without the need of an additional exporter, the Microsoft Excel files exported from Proteome Discoverer can be used directly as evidence files within XMAS.
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