How WYPT Aided in the Structure Solution of P1 from <i>Pseudomonas aeruginosa</i>
Bibliographic record
Abstract
Following the “Would You Publish This” session of the 2023 American Crystallographic Association conference where issues in solving the phase problem of the P1 pilin from Pseudomonas aeruginosa were presented and discussed, advice was taken in using an AlphaFold model to perform molecular replacement (MR). Diffraction data collection occurred in 2004, and raw image files were lost over the decades; only the merged structure files remained. Previously the phase problem was attempted to be solved with multiple isomorphous replacement with phasing from heavy atom soaks, as well as MR with a structural homolog, the P. aeruginosa pilin K122. The phase problem was solved by performing MR using an optimized AlphaFold model created using the ‘process predicted model’ program on ccp4i2 (Figure 1). This session will go over initial issues with data processing, including an issue with non-crystallographic symmetry detection, and how an optimal MR model was chosen. The final model was refined at 1.3 Å and will be discussed.
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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 | 0.003 | 0.006 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.003 | 0.003 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.002 | 0.004 |
| Insufficient payload (model declined to judge) | 0.035 | 0.012 |
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".