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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: ...@@ -576,12 +576,15 @@ The contents of each output file are as follows:
structure, after performing an Amber relaxation procedure on the unrelaxed structure, after performing an Amber relaxation procedure on the unrelaxed
structure prediction (see Jumper et al. 2021, Suppl. Methods 1.8.6 for structure prediction (see Jumper et al. 2021, Suppl. Methods 1.8.6 for
details). details).
* `ranked_*.pdb` – A PDB format text file containing the relaxed predicted * `ranked_*.pdb` – A PDB format text file containing the predicted structures,
structures, after reordering by model confidence. Here `ranked_0.pdb` should after reordering by model confidence. Here `ranked_i.pdb` should contain
contain the prediction with the highest confidence, and `ranked_4.pdb` the the prediction with the (`i + 1`)-th highest confidence (so that
prediction with the lowest confidence. To rank model confidence, we use `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 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 * `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 used to perform the model ranking, and a mapping back to the original model
names. names.
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