.. _tutorials Tutorials - Usage: ================== We provide tutorials that walk through the process of sector identification for three protein families: the Ras-like small G-proteins, the metabolic enzyme Dihydrofolate Reductase (DHFR), and the antibiotic resistance enzyme Beta-lactamase. To run the SCA calculations for all three examples, you can execute the following shell script: >>> ./runAllNBCalcs.sh For each example, this will generate the following outputs in the Outputs/ directory: 1. A pickle database (\*.db file) that contains the results of the calculations (these are then read in and analyzed in the ipython notebooks - \*.ipynb) 2. A \*.log file that provides some information about the analysis 3. A processed alignment (\*.fasta file) resulting from the scaProcessMSA script. Following this step, you can begin the tutorial as an interactive ipython notebook from the command line as follows: >>> ipython notebook SCA_G.ipynb This should open the notebook in a browser window, where you can run the code, and examine the SCA results. Tutorials - Examples: ===================== .. toctree:: :maxdepth: 1 SCA_G SCA_S1A SCA_DHFR SCA_betalactamase