embuild.md
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+#!/usr/bin/env bash
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+
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+## SBGrid EMBuild example - EMD-0346
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+## http://huanglab.phys.hust.edu.cn/EMBuild/
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+## Args: none
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+##
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+## James Vincent - biogrids.org
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+## vincent@hkl.hms.harvard.edu
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+## Mar 08, 2023
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+
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+:<<ACKNOWLEDGE
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+
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+If your use of SBGrid compiled software was an important element in
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+your publication, please include the following statement in your work:
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+"Software used in the project was installed and configured by SBGrid
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+(cite: eLife 2013;2:e01456, Collaboration gets the most out of software.)
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+
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+ACKNOWLEDGE
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+
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+# BCH E2 slurm
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+#SBATCH --partition=bch-gpu
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+#SBATCH --gres=gpu:Tesla_K:1
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+#SBATCH --mem-per-cpu=24G
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+#SBATCH --time=01:00:00
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+#SBATCH --job-name=JV-embuild
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+
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+
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+# STRIDE dependency must be downloaded/installed by user
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+curl -kLO http://webclu.bio.wzw.tum.de/stride/stride.tar.gz
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+# Untars in current directory - make a subdir first
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+mkdir stride
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+mv stride.tar.gz stride
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+cd stride
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+tar zxf stride.tar.gz
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+make
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+# Absolute stride path required in call to EMBuild
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+stride_path=`pwd`/stride
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+echo "STRIDE path: ${stride_path} "
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+cd ..
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+
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+
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+# Load cuda
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+module load cuda/11.2
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+
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+# Start SBGrid environment
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+source /programs/sbgrid.shrc
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+
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+# MCP dir needed in calls
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+mcp_dir=/programs/x86_64-linux/embuild/1.0/bin/mcp
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+
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+# embuild requires large ulimit - segfault otherwise
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+ulimit -s 1048576
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+
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+
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+# Download example data
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+curl -kLO http://huanglab.phys.hust.edu.cn/EMBuild/6N52.tgz
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+tar zxf 6N52.tgz
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+cd ./6N52/
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+
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+python.embuild ${mcp_dir}/mcp-predict.py -i emd_0346.map -o 0346_MC.mrc -m ${mcp_dir}/model_state_dict
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+
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+SWORD -i 6N52_A_AF2.pdb -m 15 -v > 6N52_A_AF2_SWORD.out
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+SWORD -i 6N52_B_AF2.pdb -m 15 -v > 6N52_B_AF2_SWORD.out
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+
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+asgdom 6N52_A_AF2.pdb 6N52_A_AF2_SWORD.out 6N52_A_AF2_doms.pdb
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+asgdom 6N52_B_AF2.pdb 6N52_B_AF2_SWORD.out 6N52_B_AF2_doms.pdb
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+
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+cat *_doms.pdb > init_chains.pdb
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+
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+EMBuild 0346_MC.mrc init_chains.pdb 4.0 6N52_EMBuild.pdb
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+
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+rearrangepdb 6N52_EMBuild.pdb 6N52_EMBuild_rearranged.pdb
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+
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+EMBuild 0346_MC.mrc 6N52_EMBuild_rearranged.pdb 4.0 6N52_EMBuild_scored.pdb \
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+ --score -stride ${stride_path}
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