Convert EOM output to a full atom PDB files
EOMv3.0 genrates cif that you can convert to full atom pdb files :
1 - Converts CIF files to PDB format using Open Babel. 2 - Creates peptide bonds and links C-alpha dummy atoms using PD2. 3 - Optimises side-chain conformations using Scwrl4.
- Python 3.x
Python packages: 1- Open Babel
conda install openbabel
2- tqdm
conda install tqdm
External programs:
1- PD2
https://github.com/jmacdona/pd2_public
To install PD2 you need:
For LINUX and MAC:
1- You need to update the SConstruct file and change all the print fonction
example print("INFO: compiling with gprof flags")
For LINUX only :
2- you need to change the name of the liboost by removing the "-mt", because liboost change its name
For Mac only
2 -In src/external/include/eigen replace the file by the last version on GitHub
https://github.com/libigl/eigen
3- Add -mt for boost_thread
For LINUX and MAC: In your .bashrc add something like export PATH=$PATH:/location/of/PD2/bin export PD2_DB=/location/of/PD2/database 2- Scwrl4
http://dunbrack.fccc.edu/lab/scwrl
In your .bashrc add something like export PATH=$PATH://location/of/Scwrl4 export SCWRL_DB=/location/of/Scwrl4.ini
Ensure you set up properly the environment variables PD2_DB and SCWRL_DB to point to the respective database directories. Run the script by providing the path of the folder where the CiFS are and the sequence in fasta format as a command-line argument:
python script_name.py path_to_sequence.fasta path_to_CIFS_FOLDER
In the sequence file if the aa are in lower case they will be untouched by SCWRL4.
The script will convert CIF files to PDB format, perform protein structure refinement, optimize side-chain conformations, and generate output PDB files in the final_pdb/ directory.
2023 JMB