embuild

EMBuild 1.0 example

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

STRIDE must be installed by user

The STRIDE program needed by EMBuild cannot be distributed with SBGrid. Users must download this themselves. An example is provided in the script below.

#!/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}