A notebook for generating a PSSM for a protein based on a PDB file.
This is a demo and is intended to run quickly.
Because of this, all calculations are performed with a fixed backbone.
In a real-world situation, it may be wiser to replace the fixed-backbone side-chain packing runs with a call to FastRelax in order to capture small backbone movements.
This notebook relies on an addon to PyRosetta currently being developed by Alex Ford.
The environment.yml file specifies the packages that are required, including a pip-installable version of Alex's code.
To create the environment, cd to the pyrosetta.distributed directory and issue the following command:
conda env update -f environment.ymlNote: if you are on the digs (i.e. you're in the Baker Lab), you will probably not have conda in your path by default.
Here's what you should do:
If it doesn't exist, create ~/bin and change to it by issuing
mkdir ~/bin && cd ~/binThen we will make a few symlinks to relevant anaconda executables by issuing
ln -s /software/miniconda3/bin/activate /software/miniconda3/bin/conda /software/miniconda3/bin/deactivate .Finally, prepend $HOME/bin to your $PATH variable in your (probably) .bashrc file by adding the following line:
export PATH=$HOME/bin:$PATHOnce the environment is configured, you will have conda: pyrosetta.distributed as a kernel option in your jupyter server.