Software for automatic detection and measurement of coiled coils in PDB structures.
- DSSP 2.3.0
- Socket
- Python 3.7.x (recommended 3.7.7)
- (optional) Pymol. For installation instructions see https://pymolwiki.org/index.php/Linux_Install
- Download and install DSSP and Socket (links above). Important: SamCC-Turbo does not work with DSSP versions 3.x (format incompatibility issues between DSSP and Socket). We recommend DSSP version 2.3.0
- Install virtualenv
pip install virtualenv- Create new virtual environment. Please ensure that you are using Python 3. You may need to install python3-venv package. Remember that when creating virtualenv you can specify version of Python to be used with --python argument (we currently recommend Python 3.7.7)
python -m venv samcc_turbo- Enter directory of your environment and activate it
cd samcc_turbo # virtual environment
source bin/activate- Install SamCC-Turbo from pip
pip install samcc-turbo- Basic usage (measure PDB, do not save pymol session)
from samcc import SamCC
sc = SamCC(bin_paths={'dssp':'/path/to/dssp', 'socket':'/path/to/socket'})
sc.run_samcc_turbo(pdbpath='/path/to/pdb', outpath='/path/to/results', save_pse=False) # to save pymol session change save_pse to True- Commands: to obtain full list of commands for SamCC-Turbo:
from samcc import SamCC
help(SamCC)- For advanced example see the Example.ipynb notebook!
Please visit https://lbs.cent.uw.edu.pl/ccdb and https://lbs.cent.uw.edu.pl/samcc_turbo
Please check our papers:
- DeepCoil-a fast and accurate prediction of coiled-coil domains in protein sequences.
- Variability of the core geometry in parallel coiled-coil bundles.
- The Structure and Topology of α-Helical Coiled Coils.
- Designability landscape reveals sequence features that define axial helix rotation in four-helical homo-oligomeric antiparallel coiled-coil structures.
If you encounter any problems with the installation or running SamCC-Turbo, please do not hesitate to contact us at s.dunin-horkawicz@uw.edu.pl or stanislaw.dunin-horkawicz@tuebingen.mpg.de