From 6a551339656c9f26d2d5b93aaff40527d81c5a7a Mon Sep 17 00:00:00 2001 From: Micha Birklbauer Date: Mon, 5 Feb 2024 16:23:01 +0100 Subject: [PATCH 1/2] add xlms-tools --- README.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/README.md b/README.md index 4ba517b..4da9169 100644 --- a/README.md +++ b/README.md @@ -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** @@ -202,6 +204,12 @@ 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](https://github.com/BobSchiffrin/PyXlinkViewer)) to export your results +for XLMS-Tools. + ## 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. From bb847b1c6b4cd5b17c02079a3e7d2f81d6468bdd Mon Sep 17 00:00:00 2001 From: Micha Birklbauer Date: Mon, 5 Feb 2024 16:25:11 +0100 Subject: [PATCH 2/2] formatting --- README.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 4da9169..14f443a 100644 --- a/README.md +++ b/README.md @@ -47,7 +47,7 @@ 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** +- **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. @@ -207,8 +207,7 @@ pyXlinkViewerExporter_msannika.exe "202001216_nsp8_trypsin_XL_REP1.xlsx" "202001 ## 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](https://github.com/BobSchiffrin/PyXlinkViewer)) to export your results -for XLMS-Tools. +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)