Commit 6aefa986 authored by Gustaf Ahdritz's avatar Gustaf Ahdritz Committed by Sachin Kadyan
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Fix typos

parent 3c240cb3
......@@ -233,14 +233,14 @@ at once. The `run_pretrained_openfold.py` script can enable this config option w
`--long_sequence_inference` command line option
#### Single-Sequence Model Inference
To run inference for a sequence using the single sequence model, first you would need the ESM1-b embedding for the sequence. For this you need to set up the ESM model on your system ([ESM](https://www.github.com/facebookresearch/esm.git)). Once you have the the setup ready, use the following command in the ESM model directory to generate an embedding:
To run inference for a sequence using the single-sequence model, first you would need the ESM-1b embedding for the sequence. For this you need to set up the ESM model on your system ([ESM](https://www.github.com/facebookresearch/esm.git)). Once you have the the setup ready, use the following command in the ESM model directory to generate an embedding:
```bash
cd <esm_dir>
python scripts/extract.py esm1b_t33_650M_UR50S <fasta> output_dir --include per_tok
```
Once you have the `*.pt` embedding file, you can place it in that sequence's alignments directory (same as that used by the MSA model of OF). That is, inside the top-level alignments directory, there will be one subdirectory for each sequence you want to run inference on, like so: `alignments_dir/{sequence_id}/{sequence_id}.pt`. You can also place a `*.hhr` files in the same directory, which can contain the details about the structures that you want to use as templates.
Once you have the `*.pt` embedding file, you can place it in that sequence's alignments directory (same as that used by the MSA model of OF). That is, inside the top-level alignments directory, there will be one subdirectory for each sequence you want to run inference on, like so: `alignments_dir/{sequence_id}/{sequence_id}.pt`. You can also place a `*.hhr` file in the same directory, which can contain the details about the structures that you want to use as templates.
Now, you are ready to run inference:
```bash
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