FindSurfaceCharge
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| Type | Python Module |
|---|---|
| Download | findSurfaceResiduesListCharged.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
findSurfaceResiduesListCharged [pH=7.0 [, folded=True [, selection=all [, cutoff=2.5 ]]]
Arguments
- 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.
- selection = str: The object or selection for which to find exposed residues {default: all}
- 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, async=0
findSurfaceResiduesListCharged
# see how pH changes the protein surface charge:
findSurfaceResiduesListCharged(7.0)
The expected surface charge of this protein at pH 7.0 is: -2.55
findSurfaceResiduesListCharged(7.0, False)
The expected charge of this denatured protein at pH 7.0 is: +0.26
findSurfaceResiduesListCharged[10.0]
The expected surface charge of this protein at pH 10.0 is: -14.19