Update alphafold.md

content/en/Manuals/hpc_cluster/selected_software/alphafold.md

@@ -24,11 +24,12 @@ singularity shell --nv $ALPHAFOLD_SING
 
 ### Using Alphafold Databases
 
-When running the alphafold command, you will be asked for certain databases. These databases can be found under the path $DATABASE_DIR/alphafold/2.1.2.
+When running the alphafold command, you will be asked for certain databases. These databases can be found under the path $DATABASE_DIR/alphafold/<version>. They can also be accessed using the `$$ALPHAFOLD_DB` environment variable that is automatically set after loading the alphafold module.
 
-Here is an example of how to write your alphafold command :
+Here is an example of how to write your alphafold command using the monomer preset:
 ```bash
 python3 /app/alphafold/run_alphafold.py \
+--model_preset=monomer \
 --db_preset=reduced_dbs \
 --use_gpu_relax=True \
 --data_dir=$DATABASES_DIR/alphafold/2.1.2 \
@@ -43,6 +44,27 @@ python3 /app/alphafold/run_alphafold.py \
 --pdb70_database_path=$DATABASES_DIR/alphafold/2.1.2/pdb70/pdb70 \
 --fasta_paths=<path to fasta file here> \
 --output_dir=<path to output directory>
+```
 
+and an example using the multimer preset:
+```bash
+python3 /app/alphafold/run_alphafold.py \
+--model_preset=multimer \
+--db_preset=reduced_dbs \
+--use_gpu_relax=True \
+--data_dir=$DATABASES_DIR/alphafold/2.1.2 \
+--uniref90_database_path=$DATABASES_DIR/alphafold/2.1.2/uniref90/uniref90.fasta \
+--mgnify_database_path=$DATABASES_DIR/alphafold/2.1.2/mgnify/mgy_clusters_2018_12.fa \
+--template_mmcif_dir=$DATABASES_DIR/alphafold/2.1.2/pdb_mmcif/mmcif_files \
+--max_template_date=2020-05-14 \
+--obsolete_pdbs_path=$DATABASES_DIR/alphafold/2.1.2/pdb_mmcif/obsolete.dat \
+--small_bfd_database_path=$DATABASES_DIR/alphafold/2.1.2/small_bfd/bfd-first_non_consensus_sequences.fasta \
+--uniprot_database_path=$ALPHAFOLD_DB/uniprot/uniprot.fasta \
+--pdb_seqres_database_path=$ALPHAFOLD_DB/pdb_seqres \
+--fasta_paths=<path to fasta file> \
+--output_dir=<path to output directory>
 ```
-Remember to fill in your fasta path and output dir if you wish to use this template.
+
+Remember to fill in your fasta path and output dir if you wish to use these templates.
+
+Additionally, these are not the only two methods of running AlphaFold, and different modes might require different sets of arguments to be passed to `alphafold.py`. For more details regarding what parameters are available, as well as more examples, please refer to the [Alphafold Github Repo](https://github.com/deepmind/alphafold).