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OpenDAS
OpenFold
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4a6c9bf1
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4a6c9bf1
authored
Jul 15, 2022
by
Gustaf Ahdritz
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GitHub
Jul 15, 2022
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Update README
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@@ -153,14 +153,13 @@ If you've already computed alignments for the query, you have the option to
skip the expensive alignment computation here with
`--use_precomputed_alignments`
.
Exactly one of
`--openfold_checkpoint_path`
or
`--jax_param_path`
must be specified
to run the inference script. These accept .pt/DeepSpeed OpenFold checkpoints
and AlphaFold's .npz JAX parameter files, respectively. For a breakdown of the
differences between the different parameter files, see the README downloaded to
`openfold/resources/openfold_params/`
. Since OpenFold was trained under a
newer training schedule than the one from which the
`model_n`
config
presets are derived, there is no clean correspondence between
`config_preset`
settings and OpenFold checkpoints; the only restraint is that
`*_ptm`
`--openfold_checkpoint_path`
or
`--jax_param_path`
accept comma-delineated lists
of .pt/DeepSpeed OpenFold checkpoints and AlphaFold's .npz JAX parameter files,
respectively. For a breakdown of the differences between the different parameter
files, see the README downloaded to
`openfold/resources/openfold_params/`
. Since
OpenFold was trained under a newer training schedule than the one from which the
`model_n`
config presets are derived, there is no clean correspondence between
`config_preset`
settings and OpenFold checkpoints; the only restraint is that
`*_ptm`
checkpoints must be run with
`*_ptm`
config presets.
Note that chunking (as defined in section 1.11.8 of the AlphaFold 2 supplement)
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