pHmap

Software for generating a surface charge based pH-profile map.

Check out the Medium story.

Optionally activity data can be visualised as lollipop bars.

Requirements

• PDB2PQR - for calculation of protonation states
• ABPS - for calculation of electrostatic surface
• PyMol - for generating surface visualization and .pngs
• ImageMagick - for generating final multi .png picture
• Argbash (argument parser generator)

Citation

Breslmayr, E. (2021). pHmap - A tool for automatized calculation and visualization of protein surface charge pH-profiles (Version v1.2). Zenodo. http://doi.org/10.5281/zenodo.4751499

Installation

• Tested under Ubuntu_20, Ubuntu_16, MacOSx_Catalina_10.15.7 and Windows10 via WSL with Ubuntu_20
• Programs: APBS_v3.0.0; pdb2pqr_v2.1.1; pymol_v2.3 & v2.4; ImageMagick 6.9.7-4 Q16 x86_64 & 7.0.10-45 Q16 x86_64

SourceCode compiling

• Template file can be changed and converted to executable code (tested with argbash_2.10)

  argbash pHmap.template -o pHmap

• Completion file add to /etc/bash_completion.d/

argbash pHmap.template --type completion --strip all -o pHmap.m4

• Required programs have to be in executable paths

PDB2PQR

• Download from Github: pdb2pqr_2.1.1
• Install

ABPS

• Download from Github: ABTS_v3.0.0
• Install

PyMol

• Open Source PyMol v2.x
• Ubuntu

sudo apt install pymol

• Mac

brew install brewsci/bio/pymol

ImageMagick

• Ubuntu

sudo apt-get install imagemagick

• Mac

brew install imagemagick

• Commands