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.yml
Note: 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 ~/bin
Then 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:$PATH
Once the environment is configured, you will have conda: pyrosetta.distributed
as a kernel option in your jupyter server.