examples/rosettafold_all_atom.md
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-## Rosettafold-All-Atom Example
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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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-ROSETTAFOLDAA_X
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-ROSETTAFOLD_DB_PATH
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-RFAA_DIR
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-DGLBACKEND
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-In addition, the script below uses a project directory that needs to be set or changed:
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-MY_PROJ_DIR=/path/to/my/project
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-The example script expects two files in the current directory:
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-[sbgrid_example.yaml](sbgrid_example.yaml)
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-and
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-[sbgrid_example.fasta](sbgrid_example.fasta)
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-We purposely renamed these example files to be sure we're using our own files and not the examples files that come with RFAA.
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-sbgrid_example.yaml is protein.yaml and base.yaml from the RFAA config/infernec 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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#!/usr/bin/env bash
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## SBGrid RosettaFold-All-Atom example
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#SBATCH -p gpu_quad
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#SBATCH --gres=gpu:1
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-MY_PROJ_DIR=<project directory>
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-cd ${MY_PROJ_DIR}
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-
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-module load cuda/11.2
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# Start SBGrid environment
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source /programs/sbgrid.shrc
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export ROSETTAFOLDAA_X=bf21483
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# Set critical env variables
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-export DGLBACKEND=pytorch
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-export ROSETTAFOLD_DB_PATH=/n/shared_db/RoseTTAFold
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+export ROSETTAFOLD_DB_PATH=/programs//local/rosettafold
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export RFAA_DIR=/programs/x86_64-linux/rosettafoldaa/${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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