PyMIV

PyMIV: A Pymol Plugin as a Molecular Interactions Viewer (MIV) of disulfide bonds, WC/Non-WC bonds, protein secondary structure etc.

Prerequisites

• conda OR

• [homebrew] (https://brew.sh/)

• [PyMOL-open-source-vewier] (git@github.com:schrodinger/pymol-open-source.git)

• [PyMOL-open-source-vewier] (https://anaconda.org/conda-forge/pymol-open-source)

• [wxPython] (https://formulae.brew.sh/formula/wxpython)

Adding PyMIV to PyMOL

In PyMOL window, go to Plugin -> Plugin manager -> Install new plugin, choose PyMIV.zip and click OK on the next step. You will then see a pop-up message Plugin "PyMIV" has been installed.

Using PyMIV

Open PyMOL

Launch PyMOL (https://pymolwiki.org/index.php/Launching_PyMOL)

Run PyMIV through Plugin -> PyMIV

PyMIV Tabs

PyMIV has six tabs and one Done button.

• The first tab Browse is to select a valid PDB format file anywhere on the user's computer. Access peptide and nucleic acid structures in PDB format at RCSB Protein Data Bank (https://www.rcsb.org/)

• The second tab Disulfide Finder includes the command for finding disulfide bodns in a polypeptide structure. This works for peptides

• The third tab End to End Distance will calculate the end to end distance of peptide and load the structure into the viewer. A measurement distance between the C-alpha carbon of the first and last amino acid will be displayed. This works for peptides

• The fourth tab WC vs Non-WC performs measurements to find nucleotide interactions in nucleic acids that abide watson-cick(e.g. A-T and G-C) interactions and non-watson-crick interactions(e.g.g G-G and U-C), displays the results in the PyMOL Viewer. This works for both DNA and RNA

• The fifth tab Alpha Helix will generate a FASTA sequence of a peptide and display with an H under amino acid resiues that are in a alpha helix secondary structure. The PDB structure will be loaded into the viewer and the alpha helices will be displayed in pink

• The sixth tab Calculate MW calculates the molecular weight of the given molecule. This works for peptides

Files

• PDB_Files contains test PDB format files

• PML_Files contains test PML format files to be run by PyMOL

• PyMIV_GUI python code for PyQt graphical user interface

• __init__.py python code to initialize PyMIV plugin into PyMOL

• calc_miv.py python code to calculate PDB data

Author Notice

• Created by Maranda McDonald and published on May 7 2023

• Insipitation taken from speleo3 pymol2-demo-plugin from the PyMOLWiki (https://pymolwiki.org/index.php/Plugins_Tutorial)