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Commit a54b34c1 authored by Hamish Tomlinson's avatar Hamish Tomlinson Committed by Copybara-Service
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Improve readme explanation of ranked_*.pdb.

PiperOrigin-RevId: 511185129
Change-Id: I035bff2f22d5b863771711f300de335e4fb3e396
parent 502d7a19
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......@@ -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.
......
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