From 08368469c3025b56fe4ed8db7a3cc40e86b03e1e Mon Sep 17 00:00:00 2001 From: Melih Yilmaz <32707537+melihyilmaz@users.noreply.github.com> Date: Thu, 19 Sep 2024 10:51:42 -0700 Subject: [PATCH] Update docs with model weights --- docs/getting_started.md | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/docs/getting_started.md b/docs/getting_started.md index 73cbd5f0..b9b8e5b5 100644 --- a/docs/getting_started.md +++ b/docs/getting_started.md @@ -81,9 +81,12 @@ This model file or a custom one can then be specified using the `--model` comman Not all releases will have a model file included on the [Releases page](https://github.com/Noble-Lab/casanovo/releases), in which case model weights for alternative releases with the same major version number can be used. -The most recent model weights for Casanovo version 3.x are currently provided under [Casanovo v3.0.0](https://github.com/Noble-Lab/casanovo/releases/tag/v3.0.0): -- `casanovo_massivekb.ckpt`: Default Casanovo weights to use when analyzing tryptic data. These weights will be downloaded automatically if no weights are explicitly specified. -- `casanovo_non-enzy.checkpt`: Casanovo weights to use when analyzing non-tryptic data, obtained by fine-tuning the tryptic model on multi-enzyme data. These weights need to be downloaded manually. +The most recent model weights for Casanovo version 4.2.x are currently provided under [Casanovo v4.2.0](https://github.com/Noble-Lab/casanovo/releases/tag/v4.2.0): +- `casanovo_v4_2_0.ckpt`: Default Casanovo weights to use as described in [Melendez et al.](https://www.biorxiv.org/content/10.1101/2024.05.16.594602v1). These weights will be downloaded automatically if no weights are explicitly specified. + +Alternatively, model weigths for Casanovo version 4.x as described in [Yilmaz et al.](https://www.nature.com/articles/s41467-024-49731-x) are currently provided under [Casanovo v4.0.0](https://github.com/Noble-Lab/casanovo/releases/tag/v4.0.0): +- `casanovo_massivekb.ckpt`: Casanovo weights to use when analyzing tryptic data. These weights need to be downloaded manually. +- `casanovo_nontryptic.ckpt`: Casanovo weights to use when analyzing non-tryptic data, obtained by fine-tuning the tryptic model on multi-enzyme data. These weights need to be downloaded manually. ## Running Casanovo