Dimpyplot

A Python frontend to the LigPlot+ program, allowing batch processing of Protein Data Bank (PDB) files through the DIMPLOT algorithm.

Requirements

1. UNIX / Linux / MacOS X
2. Python 3.7
3. Install LigPlot+ from the EBI: http://www.ebi.ac.uk/thornton-srv/software/LigPlus/
4. Download components.cif from the PDB: ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif
5. Ability to cd in the Terminal

How to Use

1. Copy dimpyplot.py to the directory containing the PDB files you want to process (the working directory), or your $PATH.

2. Run: you can run either ligplot, dimplot or both.

   • python3 dimpyplot.py --fullreport (ligplot + dimplot)
   • python3 dimpyplot.py --ligplot
   • python3 dimpyplot.py --dimplot

   default parameteres:

   --LigPlus_path /Users/yuyuan/bin/LigPlus
   --components_cif /Users/yuyuan/bin/LigPlus/data/components.cif
   --ligplot_plus /Users/yuyuan/bin/LigPlus/lib/exe_mac64/
   --wkdir ./test_pdb
   --chain1 A
   --chain2 B

3. This tool will process every PDB file in the working directory, generating new PDB files of the interaction surface, and PostScript visulization files.

Notes

• You can run python3 dimpyplot.py -h for help.

Dimpyplot + Chord Plot

With dimpyplot, you will get a series of interactions between two chains of protein complex. Chord plot is a kind of visualization to show which residues play an important role between protein interfaces.

• Red line represents H-bond interactions.
• Green-tone line represents hydrophobic interactions.

Requirements

1. Any requirements from dimpyplot
2. Python3 packages: pandas, os and dependencies
3. R 3.6.1 or above
4. R packages: magrittr=1.5, circlize=0.4.13, optparse=1.7.1 and dependencies

How to Use

Run in python3: you can change variables to fit to your pdb chain & name.

• wkdir: destinate where your pdb located.
• pdb_name: indicate which pdb your want to analysis in your pdb.
• chain1: which chain do you want to analysis in your pdb.
• chain2: the other chain you want to anlysis in your pdb.
• chain1_name: you can name as you want.
• chain2_name: you can name as you want.

Python3 script:

from dimpyplot_chord import dimplot_chord

wkdir = './test_pdb'                #change here
pdb_name = '7a91_delta_npt_noPBC'   #change here
chain1 = 'A'                        #change here
chain2 = 'B'                        #change here
chain1_name = 'hACE2'               #change here
chain2_name = 'S1RBD'               #change here

dimplot_chord(wkdir, pdb_name, chain1, chain2, chain1_name, chain2_name)