Current developments in <i>Coot</i> for macromolecular model building of Electron Cryo‐microscopy and Crystallographic Data
Bibliographic record
Abstract
Coot is a tool widely used for model building, refinement, and validation of macromolecular structures. It has been extensively used for crystallography and, more recently, improvements have been introduced to aid in cryo-EM model building and refinement, as cryo-EM structures with resolution ranging 2.5-4 A are now routinely available. Model building into these maps can be time-consuming and requires experience in both biochemistry and building into low-resolution maps. To simplify and expedite the model building task, and minimize the needed expertise, new tools are being added in Coot. Some examples include morphing, Geman-McClure restraints, full-chain refinement, and Fourier-model based residue-type-specific Ramachandran restraints. Here, we present the current state-of-the-art in Coot usage.
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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 | 0.012 | 0.017 |
| Meta-epidemiology (narrow) | 0.004 | 0.002 |
| Meta-epidemiology (broad) | 0.004 | 0.003 |
| Bibliometrics | 0.004 | 0.010 |
| Science and technology studies | 0.002 | 0.002 |
| Scholarly communication | 0.008 | 0.007 |
| Open science | 0.010 | 0.005 |
| Research integrity | 0.004 | 0.007 |
| Insufficient payload (model declined to judge) | 0.026 | 0.040 |
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".