FindSurfaceCharge

Type	Python Module
Download	findSurfaceCharge.py
Author(s)	Teddy Warner
License	BSD-2-Clause
This code has been put under version control in the project Pymol-script-repo

Drawing upon the findSurfaceResidues script, the findSurfaceCharge script will identify and output a list of all charged residues on the surface of a selectionand calculates the ionization state of a protein at a given pH. The charge can be calculated for either a folded or denatured protein. This function is intended to be used to give buffer conditions for mass spectrometry.

Usage

   findSurfaceCharge [selection, [pH, [folded ,[cutoff]]]]

Arguments

• selection = str: The object or selection for which to find exposed residues {default: all}
• pH = float: The pH to calculate the surface charge at {default: 7.0}
• folded = bool: Whether the program should calculate the charge of a folded (True) or denatured (False) protein.
• cutoff = float: The cutoff in square Angstroms that defines exposed or not. Those atoms with > cutoff Ang^2 exposed will be considered exposed {default: 2.5 Ang^2}

Examples

• 

  Result of 4FIX.pdb at pH 7.0.

run findSurfaceResiduesListCharged.py
fetch 4FIX

findSurfaceResiduesListCharged

# see how pH changes the protein surface charge:
findSurfaceCharge("4fix",7.0)
    Exposed charged residues: 
        ERREDRKEE...
    The expected surface charge of 4fix at pH 7.0 is: +3.24

findSurfaceCharge("4fix",7.0,False)
    Charged residues: 
        HHHHHHRHERREDRKEE...
    The expected charge of denatured 4fix at pH 7.0 is: +0.13

findSurfaceCharge("4fix",10.0)
    Charged residues: ...
    The expected surface charge of 4fix at pH 10.0 is: -3.86

See Also

• findSurfaceResidues
• get_area