DomainSeeker

DomainSeeker Example Feb 26, 2025

#!/usr/bin/env bash

## SBGrid DomainSeeker example
## Args: none
##
## James Vincent  - help@sbgrid.org
## Feb 26, 2025

# 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.)


source /programs/sbgrid.shrc
export DOMAINSEEKER_X=20250204

echo -e "\n## domainseeker version info ##\n"
sbgrid-info -l domainseeker

echo -e "\n## domainseeker callable programs##\n"
sbgrid-list domainseeker

## Copy DomainSeeker provided Example directory to local dir
cp -r /programs//x86_64-linux//domainseeker/20250204/DomainSeeker/Example ./

## Run test from the DomainSeeker provided Example directory
cd Example

echo -e "\n## domainseeker sample call##\n"
fetch_pdb_pae.py protein_list.txt .

parse_with_pae.py pdb_files pae_files domain_files
fit_with_chimerax.py domain_files em_data fit_out 0.001 7 200 16
score_rank.py domain_files em_data fit_out 0.001 -0.0001 0.0001 7 16 10 50

#get_fitted_domain.py domain_dir fitout_dir domain_list