- Return to the main setup page
- Python tutorial setup page
- MD tutorial setup page
- Docking tutorial setup page
Included here are instructions to get you started with the Oxford Computational Biochemistry Homology Modelling course.
These are instructions that should be followed prior to the tutorial. These will set you started with creating the appropriate conda environment to go through the tutorial's contents. Two days have been set aside on the 10th and 11th of December to do this setup and ask questions to demonstrators where needed.
The install instructions are all contained within the tutorial notebook
homology-modelling-tutorial.ipynb. Click here to open it in your browser.
We recommend that you open it using the aforementioned link and then using a terminal
(see main setup instructions) go from Objectives through
to just before 1. Perform a multiple sequence alignment.
As part of the instructions you will be asked to create a new conda environment
named OxHomology and install various associated software.
Important note: You do not need to re-install anaconda/miniconda, this
should have already been done as part of the main setup instructions.
Please do ignore this third bullet point entry from the BEFORE YOU START instructions.
Once you have finished these instructions please remember to deactivate your conda environment within your terminal using:
conda deactivate
You can then continue with the setup of the other tutorials:
- Return to the main setup page
- Python tutorial setup page
- MD tutorial setup page
- Docking tutorial setup page
This will be done on the day of the course.
In your terminal, navigate to the Homology-Modelling folder of your local download of
this tutorial.
Then activate the OxHomology conda environment:
conda activate OxHomology
Then start a jupyter notebook instance using:
jupyter notebook
In the session that opens in your browser you can then click on homology-modelling-tutorial.ipynb
to start the tutorial notebook.
As you will have already done the setup instructions, you can jump directly to
section 1. Perform a multiple sequence alignment (although you may find it useful to review the objectives).
When you are finished, don't forget to deactivate the environment!
conda deactivate