!/usr/bin/env bash

SBGrid EMBuild example - EMD-0346

http://huanglab.phys.hust.edu.cn/EMBuild/

Args: none

James Vincent - biogrids.org

vincent@hkl.hms.harvard.edu

Mar 08, 2023

:<<ACKNOWLEDGE

If your use of SBGrid compiled software was an important element in your publication, please include the following statement in your work: "Software used in the project was installed and configured by SBGrid
(cite: eLife 2013;2:e01456, Collaboration gets the most out of software.)

ACKNOWLEDGE

BCH E2 slurm

SBATCH --partition=bch-gpu

SBATCH --gres=gpu:Tesla_K:1

SBATCH --mem-per-cpu=24G

SBATCH --time=01:00:00

SBATCH --job-name=JV-embuild

STRIDE dependency must be downloaded/installed by user

curl -kLO http://webclu.bio.wzw.tum.de/stride/stride.tar.gz

Untars in current directory - make a subdir first

mkdir stride mv stride.tar.gz stride cd stride tar zxf stride.tar.gz make

Absolute stride path required in call to EMBuild

stride_path=pwd/stride echo "STRIDE path: ${stride_path} " cd ..

Load cuda

module load cuda/11.2

Start SBGrid environment

source /programs/sbgrid.shrc

MCP dir needed in calls

mcp_dir=/programs/x86_64-linux/embuild/1.0/bin/mcp

embuild requires large ulimit - segfault otherwise

ulimit -s 1048576

Download example data

curl -kLO http://huanglab.phys.hust.edu.cn/EMBuild/6N52.tgz tar zxf 6N52.tgz cd ./6N52/

python.embuild ${mcp_dir}/mcp-predict.py -i emd_0346.map -o 0346_MC.mrc -m ${mcp_dir}/model_state_dict

SWORD -i 6N52_A_AF2.pdb -m 15 -v > 6N52_A_AF2_SWORD.out SWORD -i 6N52_B_AF2.pdb -m 15 -v > 6N52_B_AF2_SWORD.out

asgdom 6N52_A_AF2.pdb 6N52_A_AF2_SWORD.out 6N52_A_AF2_doms.pdb asgdom 6N52_B_AF2.pdb 6N52_B_AF2_SWORD.out 6N52_B_AF2_doms.pdb

cat *_doms.pdb > init_chains.pdb

EMBuild 0346_MC.mrc init_chains.pdb 4.0 6N52_EMBuild.pdb

rearrangepdb 6N52_EMBuild.pdb 6N52_EMBuild_rearranged.pdb

EMBuild 0346_MC.mrc 6N52_EMBuild_rearranged.pdb 4.0 6N52_EMBuild_scored.pdb \ --score -stride ${stride_path}