How WYPT Aided in the Structure Solution of P1 from <i>Pseudomonas aeruginosa</i>
Why this work is in the frame
A frame that forgets how it found something cannot be audited. These are the routes that admitted this work.
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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Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
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 it