ProBiSEnSe pymol plugin

ProBiSEnSe represents Protein Binding Site Ensemble Segmentation.
Adapted from MaSIF, it is a visualization tool for the feature rich surface files using PyMOL.

Example data (PDB:5N69) open in Zenodo:

Original features in masif_pymol_plugin:

• This is a PyMOL plugin to visualize the feature rich surface files generated by MaSIF.
• This plugin was used to make all the figures in the MaSIF paper.
• This code is released under an Apache License v2.0. Feel free to use this code for your own plugins.

Modified (differed) from the original source

• Adding a function to focus only on the interest pt (required the interest column in the .ply file)
• Adding a function not to show surface to increase the speed to load a file.
• Visualizing additional features in .ply files: label, pred (colored with different classes).
• Adding a function to superimpose the .ply files with pdb alignment.

How to use?

Download

First, download the zip file from GitHub:

wget https://github.com/yuyuan871111/ProBiSEnSe_pymol_plugin/releases/download/0.1.1/ProBiSEnSe_pymol_plugin.zip

Then, install the plugin using Plugin Manager in PyMOL.

1. Install New Plugin > Install from local file > Choose file... > go to the path where you download your zip file (no need to decompress) > install
2. Restart PyMOL and will be available when using console in PyMOL.

Load

If you have installed the plugin in your PyMOL, simply type:

# loadply [.ply file], [interest_pt], [ignore_surface]
loadply sample.ply, 1, 0

Alternatively:

# alternative way in PyMOL console with correct path of the package
from probiosense_pymol_plugin.loadPLY import load_ply
load_ply(filename = "sample.ply", interest_pt = 1, ignore_surface = 0)

Note that:

• filename: indicate your .ply file
• insterest_pt: if you want to draw only the regions of interest, set it 1. Otherwise, set it 0 for the whole protein. (default: 1)
• ignore_surface: if you want to draw the surface as well, set it 0. Otherwise, set it 1 to ignore the surface. (default: 0)

Test with example files

# in your pymol console
load 5N69_complex.pdb         # protein + ligand (saved in the pdb file)   
loadply 5N69_protein.ply      # protein surface file using default settings

Superimpose (for PLY)

This superimpose function is to superimpose the PLY file based on the correponding PDB file. This was implemented by superimposing sample to reference and sample.ply will be transformed using the same rotational translational matrix.

# superply [pdb_query object name], [ply_query name], [pdb_ref object name]
superply sample, sample.ply, reference

• sample is a pdb object in pymol.
• sample.ply is a cgo group, which was loaded using loadply. The sample.ply must be the surface file of the pdb file sample.
• reference is a reference pdb object in pymol to be aligned to.

Test with example files

# in your pymol console
load 5N69_complex.pdb         # load the pdb file
loadply 5N69_protein.ply      # load the ply file 

fetch 8QYR                    # fetch a reference PDB file

superply 5N69_complex, 5N69_protein.ply, 8QYR  # superimpose the ply 

Pack the script into a zip file

zip -r {filename.zip} {foldername}

# e.g.
zip -r ProBiSEnSe_pymol_plugin.zip ProBiSEnSe_pymol_plugin