Frags
Generate Fragment Picking and PSIPRED secondary structure prediction.
Requirements:
- Make sure you install PyRosetta as the website describes.
- You will also need to install Rosetta as the website describes.
- Use the following command (in GNU/Linux) to download the necessary database (NCBI's nr database - 30GB) in the correct directory for this script to run successfully (approximately 3 hours to complete):
python3 Frags.py setup
Description:
This script preforms fragment picking and PSIPRED secondary structure prediction to generate the files required for an Abinitio folding simulation (like the Robetta server but locally). If you have any comments or problems with the script feel free to email me (sari.sabban@gmail.com).
How To Use:
- Use the following command to run the script (approximately 1 hour to complete):
python3 Frags.py FILENAME.pdb
- Output files will be:
- FILENAME.fasta
- frags.200.3mers
- frags.200.9mers
- pre.psipred.ss2