diff --git a/README.md b/README.md index 1af8c720e0d575fd9424feb2757dd446cadbf81d..d66230534e3a28af9f6d1dab36915e078ea0944d 100644 --- a/README.md +++ b/README.md @@ -576,12 +576,15 @@ The contents of each output file are as follows: structure, after performing an Amber relaxation procedure on the unrelaxed structure prediction (see Jumper et al. 2021, Suppl. Methods 1.8.6 for details). -* `ranked_*.pdb` – A PDB format text file containing the relaxed predicted - structures, after reordering by model confidence. Here `ranked_0.pdb` should - contain the prediction with the highest confidence, and `ranked_4.pdb` the - prediction with the lowest confidence. To rank model confidence, we use +* `ranked_*.pdb` – A PDB format text file containing the predicted structures, + after reordering by model confidence. Here `ranked_i.pdb` should contain + the prediction with the (`i + 1`)-th highest confidence (so that + `ranked_0.pdb` has the highest confidence). To rank model confidence, we use predicted LDDT (pLDDT) scores (see Jumper et al. 2021, Suppl. Methods 1.9.6 - for details). + for details). If `--models_to_relax=all` then all ranked structures are + relaxed. If `--models_to_relax=best` then only `ranked_0.pdb` is relaxed + (the rest are unrelaxed). If `--models_to_relax=none`, then the ranked + structures are all unrelaxed. * `ranking_debug.json` – A JSON format text file containing the pLDDT values used to perform the model ranking, and a mapping back to the original model names.