--- title: "UC #1 : The XDS Reproducibility Project" url: "https://help.dectris.cloud/en/article/uc-1-the-xds-reproducibility-project" language: "en" last_updated: "2026-08-10T09:37:17.779Z" --- # UC #1 : The XDS Reproducibility Project ##### Speaker: Clemens Vonrhein - Global Phasing ## Learning objectives By the end of this workshop you will have: - Run the same dataset through both the standalone **XDS** job template and the **autoPROC** job template on DECTRIS D.LAB, and compared the results. - Learned how to override individual XDS.INP parameters through the job template, without editing the file by hand. - Seen how D.LAB captures the full context of a job — input data, software version, environment, parameters, and outputs — so any result can be traced back and reproduced. ## Available Datasets You will have access to the following datasets on DECTRIS D.LAB during the workshop: - [5RET](https://www.rcsb.org/structure/5RET) (https://zenodo.org/records/3730992) - [5RE4](https://www.rcsb.org/structure/5RE4) (https://zenodo.org/records/3730483) - [5RG0](https://www.rcsb.org/structure/5RG0) (https://zenodo.org/records/3731556) - [5RFL](https://www.rcsb.org/structure/5RFL) (https://zenodo.org/records/3731412) - [5REK](https://www.rcsb.org/structure/5REK) (https://zenodo.org/records/3730929) - [5RE7](https://www.rcsb.org/structure/5RE7) (https://zenodo.org/records/3730531) The datasets will be available in you given project under `raw/UC1_XDS_Reproducibility` Choose one dataset for your group to focus on. ## DECTRIS D.LAB Job Templates [xds\_par & generate\_XDS.INP](https://app.dectris.cloud/sections/library/jobs/templates/public?id=019fd243-92b8-7af3-a193-c0e888d61cec) - runs XDS directly from a supplied or auto-generated `XDS.INP`. [autoPROC process workshop](https://app.dectris.cloud/sections/library/jobs/templates?id=019f2877-f3ae-7c50-874d-3db097a1160b) - runs autoPROC's `process` command, which wraps XDS together with scaling, symmetry determination, and STARANISO anisotropic analysis. (The template will be made available during the workshop) ## Part 1: A first run with XDS ### Running the XDS template 1. Go to the **xds** job template. 2. Configure the path to the first image file of your chosen dataset. 3. Configure `DC_XDS_INP_PATH` to point at the `XDS.INP` file for your dataset, found under `auxiliary/UC1_XDS_Reproducibility/SAMPLE/XDS.INP`. This file specifies how `xds_par` should run. 4. Leave `DC_XDS_INPUT_FOLDER` empty. It's only used to continue from an earlier analysis (e.g. reusing an existing `SPOT.XDS`/`XPARM.XDS`) — not needed for a first run.![](https://cdn-assets.productfruits.com/5630e5db-15fb-462a-9521-97c25cd45795) 5. On the **Parameters** tab, leave every input at its default value for this first run.![](https://cdn-assets.productfruits.com/c173320d-95f0-4429-834c-97386443ea56) 6. On the **Performance** tab, select the swift machine (8 CPU, 32 GB RAM) — sufficient for the datasets in this workshop.![](https://cdn-assets.productfruits.com/53d26bd6-a8f5-4cb0-bc94-2a05f4ff538e) 7. Click on the **ADD TAG** button and write your sample name. This will help you organize your results in your Analysis Overview. 8. Click **RUN JOB**. You can follow its progress from **Analysis →** [**Overview**](https://app.dectris.cloud/sections/analysis/overview)**.** ### Inspecting the job details page The job details page has several tabs: - **Output files** — every file generated during the run, including the generated quality plots.![](https://cdn-assets.productfruits.com/20bc9701-1144-4cea-b4c0-4959137aa858) - **Output variables** — parameters extracted from the job's output, such as refined cell constants.![](https://cdn-assets.productfruits.com/cf2353a7-0c9e-4bbd-b4ad-64f97c6c77a4) - **Inputs** — every input parameter used for this run. Keeping this context means you can always trace back exactly how a result was produced.![](https://cdn-assets.productfruits.com/c2a47993-32b8-4db8-9e91-e694d9cf8513) - **Logs** — everything written to stdout during the job.![](https://cdn-assets.productfruits.com/5c453def-0db3-49a9-ad39-17acbd510429) #### Having a look at the raw data The output includes `data_viewer.html` — open it to page through a sample of raw frames from the dataset. This is a chance to check spot shape and spot any features in the data that may have affected the processing. The viewer supports scroll-to-zoom, click-and-drag panning, and Min/Max sliders to adjust contrast on the fly, so you can inspect faint features or an overexposed frame without needing to reprocess anything. ![](https://cdn-assets.productfruits.com/3581b0e5-06a3-4090-a76e-0daf7fb5dd9e) #### Look at the raw XDS output Beyond the summary quality plots, you can inspect XDS's own output files directly: from the **Output files** tab, open the `xds_output` folder to see every file XDS generated, plus the exact `XDS.INP` used for the run. ![](https://cdn-assets.productfruits.com/79c73b5f-6271-44dc-9ff3-63b6c75e4112) The various `.LP` files show, step by step, how indexing, integration, and scaling went. ![](https://cdn-assets.productfruits.com/81f2756b-dc06-42dc-ba02-fa2f85f66ff8) ## Part 2: Running autoPROC ### Running the autoPROC template 1. Go to the **autoPROC process workshop** job template. 2. On the first page, point it at the folder containing your chosen sample's data. 3. ![](https://cdn-assets.productfruits.com/b14dc26b-f921-4c57-8d3c-be0e51283d4c)On the **Parameters** page, leave `DC_CELL` and `DC_SYMM` at `-1` — this tells autoPROC to determine both automatically.![](https://cdn-assets.productfruits.com/49070fab-b5a0-41b6-bd42-911012489ab4) 4. On the last page, choose the same swift machine type as before. 5. Add a tag with your sample name, either before or after starting the job.![](https://cdn-assets.productfruits.com/98dbcdf8-aab9-4593-aa35-d7203f1d29bb) 6. Click **RUN JOB**. ### Inspecting the output In the job output folder, all output files generated by autoPROC can be found in the autoPROC subfolder. In addition, the main output folder also contains a file `0_autoPROC_summary.html`, which can be opened to view a report of the autoPROC analysis. If you click on the OPEN IN A NEW TAB button, you can get a full-page view of the html report: ![](https://cdn-assets.productfruits.com/fd1b419a-4395-4b7b-b0e7-612869436688) The html can also be downloaded and opened in a browser of your own choosing. Note however, that in either case the hyperlinks will not work. ### Discussion prompt: Differences in XDS and autoPROC output - What were the differences in the XDS output vs the autoPROC output ? - How does the XDS.INP differ between the two jobs ? - Did autoPROC flag any warnings, which you did not take into consideration in the XDS job? ## Part 3: Re-running the XDS job Based on the discussion above: what would you change in your XDS job? 1. Go back to your analysis overview table and click **rerun** on your original XDS job. This opens a run-job interface pre-filled to match your previous job.![](https://cdn-assets.productfruits.com/6c188bbf-09de-4ce7-9c68-1520d04c0ada) 2. Go to the **Parameters** tab and click **Show advanced** to reveal the parameters that override the corresponding keyword in `XDS.INP`. For example, setting `DC_XDS_SPACE_GROUP` to `150` changes `SPACE_GROUP_NUMBER=0` to `SPACE_GROUP_NUMBER=150` in `XDS.INP` before `xds_par` runs.![](https://cdn-assets.productfruits.com/0f3dbd4c-794e-4fa2-a656-06eabee2a5b1) 3. Configure whichever parameters you'd like to experiment with, then click **RERUN**. 4. ![](https://cdn-assets.productfruits.com/6525d5b2-caca-44e7-94cb-9a29c83bae72)Tag the new job with your dataset name, and optionally with the parameter(s) you're testing. 5. Inspect the results — what changed as a result of the new parameters?