Generating RMSF data

Hello! This is the protocol for running residue-by-residue RMSF analysis of a simulation system. You will need PyMOL (and its license), Python 3.9, rmsf_states.py, and plot-byres.py. You will also need the .pdb and .dcd files for your system from the VMD conversion step.

Performing RMSF analysis

1. Double-click the .pdb file to open it in PyMOL. Then, under File > Open, open the .dcd file.

2. In PyMOL's command line, run intra_fit name CA.

3. Go to File > Run script. Open rmsf_states.py.

4. In the command line, run rmsf_states yoursystemnamehere, byres=1.

5. Once that is finished, run spectrum b, blue_white_red, minimum=0, maximum=5.

6. Go to File > Save session and save your system as systemname-rmsf.pse. This .pse file contains all .pdb, .dcd, and RMSF information and can be used as a helpful visual reference later.

7. Ensure you move rmsf.txt from the folder containing rmsf_states.py to the working directory. If you put rmsf_states.py in your working directory, this direction does not apply.

8. In a terminal, cd to the working directory, then run python3 plot-byres.py. This should generate a plot and rmsf.csv.

9. Add the generated files to the Drive, and put a link to the containing folder on the COVID-19 Progress page.

Editing rmsf_states.py

When using rmsf_states.py on a new type of system, you will need to edit it. Double-click the Python script to open it in IDLE, then go to Options > Show Line Numbers. Scroll to line 134.

• If you are working with a two-chain system, edit range(21, 616) (for chain A) and range(336, 519) (for chain B) to the appropriate numbers for your system. The first number should match your first residue, and the last number should be one higher than your last residue.

• If you are working with a one-chain system, comment out (add hashtags at the beginning of) lines 138 through 140. The lines should turn red when you add the hashtags. Then, edit range(21, 616) to the appropriate numbers for your system. The first number should match your first residue, and the last number should be one higher than your last residue.