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Fix spaces after backslashes in commands #446

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Nov 6, 2024
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Fix spaces after backslashes in commands #446

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26 changes: 13 additions & 13 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -735,7 +735,7 @@ create_individual_features.py \
--data_dir=/scratch/AlphaFold_DBs/2.3.2

/ \
--output_dir=/scratch/mydir/test_AlphaPulldown/ \
--output_dir=/scratch/mydir/test_AlphaPulldown/ \
--max_template_date=2050-01-01 \
--skip_existing=True \
--seq_index=$SLURM_ARRAY_TASK_ID
Expand Down Expand Up @@ -798,9 +798,9 @@ source activate AlphaPulldown
create_individual_features.py \
--fasta_paths=<sequences.fasta> \
--data_dir=<path to alphafold databases> \
--output_dir=<dir to save the output objects> \
--output_dir=<dir to save the output objects> \
--use_mmseqs2=True \
--max_template_date=<any date you want, format like: 2050-01-01> \
--max_template_date=<any date you want, format like: 2050-01-01> \
```

#### Output
Expand Down Expand Up @@ -865,7 +865,7 @@ source activate AlphaPulldown
create_individual_features.py \
--fasta_paths=<sequences.fasta> \
--data_dir=<path to alphafold databases> \
--output_dir=<output_dir> \
--output_dir=<output_dir> \
--skip_existing=False \
--use_mmseqs2=True \
--seq_index=<any number you want or skip the flag to run all one after another>
Expand Down Expand Up @@ -940,7 +940,7 @@ create_individual_features.py \
--path_to_mmt=<path to template directory> \
--description_file=<description.csv> \
--data_dir=<path to alphafold databases> \
--output_dir=<dir to save the output objects> \
--output_dir=<dir to save the output objects> \
--max_template_date=<any date you want, format like: 2050-01-01> \
--save_msa_files=True \
--use_precomputed_msas=True \
Expand Down Expand Up @@ -1175,9 +1175,9 @@ export TF_FORCE_UNIFIED_MEMORY='1'
####
run_multimer_jobs.py \
--mode=custom \
--monomer_objects_dir=<dir that stores feature pickle files> \
--monomer_objects_dir=<dir that stores feature pickle files> \
--protein_lists=<protein_list.txt> \
--output_path=<path to output directory> \
--output_path=<path to output directory> \
--num_cycle=<any number e.g. 3> \
--data_dir=/scratch/AlphaFold_DBs/2.3.2/ \
--num_predictions_per_model=1 \
Expand Down Expand Up @@ -1280,10 +1280,10 @@ To run `run_multimer_jobs.py` in `pulldown` mode, use the following script:
```bash
run_multimer_jobs.py \
--mode=pulldown \
--monomer_objects_dir=<dir that stores feature pickle files> \
--monomer_objects_dir=<dir that stores feature pickle files> \
--protein_lists=<protein_list1.txt>,<protein_list2.txt> \
--output_path=<path to output directory> \
--data_dir=<path to AlphaFold data directory> \
--data_dir=<path to AlphaFold data directory> \
--num_cycle=<any number e.g. 3>
```

Expand Down Expand Up @@ -1321,11 +1321,11 @@ To run `run_multimer_jobs.py` in `all_vs_all` mode, use the following script:
```bash
run_multimer_jobs.py \
--mode=all_vs_all \
--monomer_objects_dir=<dir that stores feature pickle files>
--monomer_objects_dir=<dir that stores feature pickle files> \
--protein_lists=<protein_list.txt> \
--output_path=<path to output directory> \
--data_dir=<path to AlphaFold data directory> \
--num_cycle=<any number e.g. 3>
--output_path=<path to output directory> \
--data_dir=<path to AlphaFold data directory> \
--num_cycle=<any number e.g. 3>
```

Compared to [2.1 Basic run](#21-basic-run), this example differs in:
Expand Down
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