23a0d3bfa8246b8f93fc515667024a1270f61a00
embuild.md
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| 1 | -#!/usr/bin/env bash |
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| 2 | - |
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| 3 | -## SBGrid EMBuild example - EMD-0346 |
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| 4 | -## http://huanglab.phys.hust.edu.cn/EMBuild/ |
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| 5 | -## Args: none |
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| 6 | -## |
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| 7 | -## James Vincent - biogrids.org |
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| 8 | -## vincent@hkl.hms.harvard.edu |
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| 9 | -## Mar 08, 2023 |
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| 10 | - |
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| 11 | -:<<ACKNOWLEDGE |
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| 12 | - |
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| 13 | -If your use of SBGrid compiled software was an important element in |
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| 14 | -your publication, please include the following statement in your work: |
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| 15 | -"Software used in the project was installed and configured by SBGrid |
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| 16 | -(cite: eLife 2013;2:e01456, Collaboration gets the most out of software.) |
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| 17 | - |
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| 18 | -ACKNOWLEDGE |
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| 19 | - |
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| 20 | -# BCH E2 slurm |
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| 21 | -#SBATCH --partition=bch-gpu |
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| 22 | -#SBATCH --gres=gpu:Tesla_K:1 |
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| 23 | -#SBATCH --mem-per-cpu=24G |
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| 24 | -#SBATCH --time=01:00:00 |
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| 25 | -#SBATCH --job-name=JV-embuild |
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| 26 | - |
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| 27 | - |
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| 28 | -# STRIDE dependency must be downloaded/installed by user |
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| 29 | -curl -kLO http://webclu.bio.wzw.tum.de/stride/stride.tar.gz |
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| 30 | -# Untars in current directory - make a subdir first |
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| 31 | -mkdir stride |
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| 32 | -mv stride.tar.gz stride |
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| 33 | -cd stride |
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| 34 | -tar zxf stride.tar.gz |
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| 35 | -make |
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| 36 | -# Absolute stride path required in call to EMBuild |
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| 37 | -stride_path=`pwd`/stride |
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| 38 | -echo "STRIDE path: ${stride_path} " |
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| 39 | -cd .. |
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| 40 | - |
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| 41 | - |
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| 42 | -# Load cuda |
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| 43 | -module load cuda/11.2 |
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| 44 | - |
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| 45 | -# Start SBGrid environment |
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| 46 | -source /programs/sbgrid.shrc |
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| 47 | - |
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| 48 | -# MCP dir needed in calls |
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| 49 | -mcp_dir=/programs/x86_64-linux/embuild/1.0/bin/mcp |
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| 50 | - |
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| 51 | -# embuild requires large ulimit - segfault otherwise |
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| 52 | -ulimit -s 1048576 |
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| 53 | - |
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| 54 | - |
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| 55 | -# Download example data |
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| 56 | -curl -kLO http://huanglab.phys.hust.edu.cn/EMBuild/6N52.tgz |
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| 57 | -tar zxf 6N52.tgz |
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| 58 | -cd ./6N52/ |
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| 59 | - |
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| 60 | -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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| 61 | - |
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| 62 | -SWORD -i 6N52_A_AF2.pdb -m 15 -v > 6N52_A_AF2_SWORD.out |
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| 63 | -SWORD -i 6N52_B_AF2.pdb -m 15 -v > 6N52_B_AF2_SWORD.out |
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| 64 | - |
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| 65 | -asgdom 6N52_A_AF2.pdb 6N52_A_AF2_SWORD.out 6N52_A_AF2_doms.pdb |
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| 66 | -asgdom 6N52_B_AF2.pdb 6N52_B_AF2_SWORD.out 6N52_B_AF2_doms.pdb |
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| 67 | - |
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| 68 | -cat *_doms.pdb > init_chains.pdb |
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| 69 | - |
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| 70 | -EMBuild 0346_MC.mrc init_chains.pdb 4.0 6N52_EMBuild.pdb |
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| 71 | - |
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| 72 | -rearrangepdb 6N52_EMBuild.pdb 6N52_EMBuild_rearranged.pdb |
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| 73 | - |
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| 74 | -EMBuild 0346_MC.mrc 6N52_EMBuild_rearranged.pdb 4.0 6N52_EMBuild_scored.pdb \ |
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| 75 | - --score -stride ${stride_path} |
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| ... | ... | \ No newline at end of file |