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- 22:35, 9 October 2026 Cctbx.xfel GUI/Troubleshooting (hist | edit) [4,532 bytes] Aaron (talk | contribs) (Created page with "{{DISPLAYTITLE:cctbx.xfel GUI/Troubleshooting}} What to check when something does not behave. The GUI prints errors and progress to the terminal it was started from, so that terminal is always the first place to look. Back to cctbx.xfel GUI. == A status light is red == A red light means that thread hit an exception and stopped; the traceback is in the terminal. Common causes: the database connection dropped (the server was restarted or the job running it ended), th...")
- 22:32, 9 October 2026 Cctbx.xfel GUI/Workflows (hist | edit) [7,859 bytes] Aaron (talk | contribs) (Created page with "{{DISPLAYTITLE:cctbx.xfel GUI/Workflows}} Step-by-step recipes for the common things done with the cctbx.xfel GUI. Each step names the tab or dialog it happens in; see the tab pages for the details of every control. Back to cctbx.xfel GUI. == Setting up a new experiment == # Start <code>cctbx.xfel</code>. In the login dialog press '''DB Credentials...''' and enter the database server, database, user and password. If you have no server, fill those in anyway and pres...")
- 22:30, 9 October 2026 Cctbx.xfel GUI/Merging Stats tab (hist | edit) [2,747 bytes] Aaron (talk | contribs) (Created page with "{{DISPLAYTITLE:cctbx.xfel GUI/Merging Stats tab}} The '''Merging stats tab''' shows the merging statistics of each version of a dataset, read from the merging job's log, and the cosym embedding plot when the merge resolved an indexing ambiguity. The ''Merging Stats Sentinel'' re-reads the logs every 5 seconds while the tab is showing, so a merge that is still running fills in as it goes. Back to cctbx.xfel GUI. == Selecting a dataset == * '''Select dataset''': the...")
- 22:28, 9 October 2026 Cctbx.xfel GUI/Datasets tab (hist | edit) [10,042 bytes] Aaron (talk | contribs) (Created page with "{{DISPLAYTITLE:cctbx.xfel GUI/Datasets tab}} The '''Datasets tab''' takes processed runs through to a merged reflection file. A '''dataset''' selects runs from a trial by tag and runs a pipeline of tasks over them: optional ensemble refinement, scaling, merging, and optionally Phenix. Each merge creates a new '''version''' of the dataset, and new versions keep appearing as further runs finish, so merged data are available while collection is still going on. Back to cc...")
- 22:19, 9 October 2026 Cctbx.xfel GUI/Unit Cell tab (hist | edit) [3,608 bytes] Aaron (talk | contribs) (Created page with "{{DISPLAYTITLE:cctbx.xfel GUI/Unit Cell tab}} The '''Unit Cell tab''' plots histograms of the unit cell parameters of every indexed lattice in a trial, so that you can check that indexing is finding the expected cell, compare samples or conditions, spot polymorphs, and define unit cell clusters for the scaling stage of a dataset to filter on. The plot is redrawn every 15 seconds by the ''Unit Cell Sentinel'' while ''Auto update'' is ticked. Back to cctbx.xfel GUI....")
- 22:18, 9 October 2026 Cctbx.xfel GUI/Run Stats tab (hist | edit) [6,057 bytes] Aaron (talk | contribs) (Created page with "{{DISPLAYTITLE:cctbx.xfel GUI/Run Stats tab}} The '''Run Stats tab''' is the live view of how processing is going: for each image of the selected runs it shows how many strong spots were found, whether the image indexed, to what resolution, and the photon energy, together with per-run hit and indexing rates. It is the tab to keep open during data collection. The plot is redrawn every 5 seconds by the ''Run Stats Sentinel'' while ''Auto update'' is ticked. Back to cctb...")
- 21:34, 9 October 2026 Cctbx.xfel GUI/Jobs tab (hist | edit) [4,729 bytes] Aaron (talk | contribs) (Created page with "{{DISPLAYTITLE:cctbx.xfel GUI/Jobs tab}} The '''Jobs tab''' lists every job the GUI has submitted, with its status in the queuing system, and provides the controls for stopping, deleting and resubmitting jobs. While the tab is showing, the '''Job Monitor''' thread queries the queuing system every 10 seconds and updates the statuses. Back to cctbx.xfel GUI. == The job table == {| class="wikitable" ! Column !! Meaning |- | '''Job''' || The job's id in the database. A...")
- 21:06, 9 October 2026 Cctbx.xfel GUI/Trials tab (hist | edit) [8,457 bytes] Aaron (talk | contribs) (Created page with "{{DISPLAYTITLE:cctbx.xfel GUI/Trials tab}} The '''Trials tab''' is where processing is set up. A '''trial''' is a numbered set of spot finding, indexing and integration parameters; each trial owns one or more '''run blocks''' that say which runs it applies to and how their images should be read. Making a trial ''active'' is what causes jobs to be submitted. Back to cctbx.xfel GUI. == Layout == Each trial is a box labelled with its number and the start of its commen...")
- 21:04, 9 October 2026 Cctbx.xfel GUI/Energy tab (hist | edit) [3,869 bytes] Aaron (talk | contribs) (Created page with "{{DISPLAYTITLE:cctbx.xfel GUI/Energy tab}} The '''Energy tab''' calibrates the per-shot photon energy at LCLS. It is shown only when the facility is LCLS and the GUI is not in monitoring mode. The tab runs its calculations in the ''Calib Worker'' thread, whose light turns yellow while a calibration is running and green when it is idle. Back to cctbx.xfel GUI. == Background == At LCLS each shot's photon energy can be measured two ways: from the electron beam energy...")
- 21:00, 9 October 2026 Cctbx.xfel GUI/Runs tab (hist | edit) [4,269 bytes] Aaron (talk | contribs) (Created page with "{{DISPLAYTITLE:cctbx.xfel GUI/Runs tab}} The '''Runs tab''' lists every run the GUI knows about and the sample tags attached to each. It is where tags are created, applied and kept up to date as runs arrive. Tags are the handles that the Run Stats, Unit Cell and Datasets tabs use to select runs, so keeping them accurate pays off later. Back to cctbx.xfel GUI. == Where...")
- 20:58, 9 October 2026 Cctbx.xfel GUI/Settings (hist | edit) [9,966 bytes] Aaron (talk | contribs) (Created page with "{{DISPLAYTITLE:cctbx.xfel GUI/Settings}} The '''Settings dialog''' is the first thing the GUI shows when it starts (titled ''CCTBX.XFEL Login'') and is also opened by the '''Settings''' toolbar button. It collects everything the GUI needs to connect to an experiment: the database, the experiment tag, the facility, the output folder, and how jobs are submitted. All of it is saved as a project. Back to cctbx.xfel GUI. == T...")
- 20:47, 9 October 2026 Cctbx.xfel GUI (hist | edit) [14,243 bytes] Aaron (talk | contribs) (Created page with "{{DISPLAYTITLE:cctbx.xfel GUI}} The '''cctbx.xfel GUI''' is the graphical front end for processing serial crystallography data with cctbx.xfel and DIALS. It watches for new runs as they are collected, submits processing jobs to a cluster or to the local machine, records everything in a database, and shows live feedback on hit rates, indexing rates, unit cells and merging statistics. It can also take a finished set of runs through ensemble refinement, scaling and merging,...")
- 22:57, 21 August 2026 Cctbx.xfel.merge (hist | edit) [17,790 bytes] Aaron (talk | contribs) (Created page with "= ''cctbx.xfel.merge'' = '''''cctbx.xfel.merge''''' is the scaling, post-refinement and merging program of cctbx.xfel. It takes the per-image integrated results produced by dials.stills_process — one crystal per still shot — and reduces the whole ensemble to a single set of merged structure-factor intensities (an MTZ file) suitable for structure solution and refinement, together with the crystallographic quality statistics (completeness, multiplicity, CC½, CC*,...")
- 22:22, 21 August 2026 Dials.stills process (hist | edit) [15,668 bytes] Aaron (talk | contribs) (Created page with "= dials.stills_process = '''dials.stills_process''' is the core data-reduction program of cctbx.xfel. It takes a set of still diffraction images — typically serial femtosecond crystallography (SFX) snapshots from an XFEL (LCLS, SACLA, EuXFEL) or still shots from a synchrotron — and reduces each one, independently, through the full DIALS pipeline: '''import → spot-finding → indexing → refinement → integration'''. Its output (integrated intensities together wi...")