examples/rosettafold_all_atom.md
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+
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+## Rosettafold-All-Atom Example
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+
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+Below we provide a sample bash script, a fasta file renamed from one of the RFAA examples and a config yaml file.
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+You must run RFAA outside of the installation directory.
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+In order to do this you must provide your own config yaml file(s) and set the location of this yaml file. We show an example using the --config-dir option from hydra.
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+These environment variables must be set:
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+ROSETTAFOLD_DB_PATH - the directory to the RosettaFold databases:
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+
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+```
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+/programs/local/rosettafold
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+├── bfd
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+│   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_a3m.ffdata
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+│   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_a3m.ffindex
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+│   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_cs219.ffdata
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+│   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_cs219.ffindex
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+│   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_hhm.ffdata
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+│   └── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_hhm.ffindex
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+├── pdb100_2021Mar03
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+│   ├── LICENSE
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+│   ├── pdb100_2021Mar03_a3m.ffdata
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+│   ├── pdb100_2021Mar03_a3m.ffindex
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+│   ├── pdb100_2021Mar03_cs219.ffdata
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+│   ├── pdb100_2021Mar03_cs219.ffindex
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+│   ├── pdb100_2021Mar03_hhm.ffdata
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+│   ├── pdb100_2021Mar03_hhm.ffindex
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+│   ├── pdb100_2021Mar03_pdb.ffdata
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+│   └── pdb100_2021Mar03_pdb.ffindex
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+└── UniRef30_2020_06
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+ ├── UniRef30_2020_06_a3m.ffdata
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+ ├── UniRef30_2020_06_a3m.ffindex
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+ ├── UniRef30_2020_06_cs219.ffdata
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+ ├── UniRef30_2020_06_cs219.ffindex
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+ ├── UniRef30_2020_06_hhm.ffdata
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+ ├── UniRef30_2020_06_hhm.ffindex
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+ ├── UniRef30_2020_06_hhsuite.tar.gz
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+ └── UniRef30_2020_06.md5sums
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+```
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+
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+
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+
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+ROSETTAFOLDAA_X - the SBGrid version of RosettaFold-All-Atom.
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+RFAA_DIR - The direcotyr where RosettaFold-All-Atom is install under SBGrid. In most cases ythe example shown in the script below will be correct.
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+
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+The example script expects two files in the current directory:
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+
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+[sbgrid_example.yaml](sbgrid_example.yaml)
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+
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+and
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+[sbgrid_example.fasta](sbgrid_example.fasta)
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+
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+We purposely renamed these example files to be sure we're using our own files and not the example files that come with RFAA.
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+sbgrid_example.yaml is protein.yaml and base.yaml from the RFAA config/inference examples directory.
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+sbgrid_example.fasta contains the 7U7W_1 protein from that same example.
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+
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+
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+```
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#!/usr/bin/env bash
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## SBGrid RosettaFold-All-Atom example
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export ROSETTAFOLDAA_X=bf21483
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# Set critical env variables
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-export ROSETTAFOLD_DB_PATH=/programs//local/rosettafold
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+export ROSETTAFOLD_DB_PATH=/n/shared_db/RoseTTAFold
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export RFAA_DIR=/programs/x86_64-linux/rosettafoldaa/${ROSETTAFOLDAA_X}/RoseTTAFold-All-Atom
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# Call the correct python bundled with RFAA
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database_params.command=${RFAA_DIR}/make_msa.sh \
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database_params.hhdb=${ROSETTAFOLD_DB_PATH}/pdb100_2021Mar03/pdb100_2021Mar03
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+```
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+