Tutorial

Follow these steps to obtain the scores for the residue pairs and then the highest scored set can be used for DEER/EPR experiments on the protein of your interest.

Extract Compatible Pairs

A word of caution, this script is a little heavy and may take long depending on the size of the dataset and we recommend that if you have access to a HPC or a cluster, you can submit it as a job via a batch scheduler. It generates a file named compatiblePairs.txt which will be needed for further steps.

~ $ ipython <sourceCodePath>/generatePairs.py <path-to-input-file/sample.inp>

Build and Score MSMs

Make sure you have the compatiblePairs.txt already generated and in the current folder.

~ $ source <sourceCodePath>/run <path-to-input-file/sample.inp>

Clean your directory

If you are sure you have obtained the correct results and the program has run without faults, you can clean your directory of temporary files using the following script. This will delete all log files generated during the program execution.

~ $ source <sourceCodePath>/clean

Now, you will see folders such as ITER1, ITER2 and so on, which contain the residue sets scored, the corresponding MSM and scored files. This Jupyter Notebook provides a guide to how you can extract the information from the data generated.