Future developments for macromolecular crystallography at the CLS
Bibliographic record
Abstract
The Canadian Macromolecular Crystallography Facility (CMCF) at the Canadian Light Source (CLS) is a suite of fully automated beamlines, 08ID-1 and 08B1-1 [1]. It serves over 60 Canadian groups plus academic and commercial users in the US. Besides remote data collection, we offer Mail-In service where data are collected by CMCF staff. Beamline 08B1-1 has been in operation since 2011 and beamline 08ID-1 since 2006. When beamline 08ID-1 was designed, over 10 years ago, small crystals were defined as having sizes of 50-100 μm. Today, the most challenging experiments require more intense X-ray beams that can be focused to accommodate much smaller crystal sizes of less than 5 μm with flux on the order of 10^11 photons/s. To reach these stringent parameters, a new more powerful source of X-rays will be required, which will be provided by a longer small-gap in-vacuum undulator (SGU). To accommodate the higher power levels and to focus X-rays to a smaller focal spot with a high degree of spatial and temporal stability, the existing X-ray optical elements need to be upgraded. The remaining components of the project include a 5-axis alignment table for improving alignment of small samples with the microbeam, a high-efficiency robotic sample-changer and a single-photon X-ray detector. Several options for the new design will be discussed. These developments are consistent with the current direction of structural biology research at the CLS [2]. Since 2006 over 225 (240) papers and 400 (444) PDB deposits reported data collected at beamline 08ID-1. Parentheses indicate the total number for the CMCF. Many of these have been published in very high impact journals such as N. Engl. J. Med., Nature, Cell, Science, PNAS, among others (http://cmcf.lightsource.ca/publications/).
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.028 | 0.012 |
| Meta-epidemiology (narrow) | 0.003 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.002 |
| Bibliometrics | 0.004 | 0.004 |
| Science and technology studies | 0.003 | 0.003 |
| Scholarly communication | 0.005 | 0.008 |
| Open science | 0.007 | 0.004 |
| Research integrity | 0.006 | 0.007 |
| Insufficient payload (model declined to judge) | 0.102 | 0.048 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".