Difference between revisions of "FindSurfaceCharge"
Jump to navigation
Jump to search
TeddyWarner (talk | contribs) m (TeddyWarner moved page FindSurfaceResiduesListCharged to FindSurfaceCharge: Significantly changed function) |
TeddyWarner (talk | contribs) (Changed function significantly) |
||
| Line 6: | Line 6: | ||
}} | }} | ||
| − | + | 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 = | = Usage = | ||
| − | findSurfaceResiduesListCharged [pH=7.0 [, selection=all [, cutoff=2.5 | + | findSurfaceResiduesListCharged [pH=7.0 [, folded=True [, selection=all [, cutoff=2.5 ]]] |
= Arguments = | = Arguments = | ||
* '''pH''' = float: The pH to calculate the surface charge at {default: 7.0} | * '''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} | * '''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} | * '''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 = | = Examples = | ||
<gallery> | <gallery> | ||
| − | File: | + | File:SurfaceCharge.PNG|Result of 4FIX.pdb at pH 7.0. |
</gallery> | </gallery> | ||
| Line 34: | Line 32: | ||
# see how pH changes the protein surface charge: | # see how pH changes the protein surface charge: | ||
| − | findSurfaceResiduesListCharged | + | findSurfaceResiduesListCharged(7.0) |
| − | The expected surface charge of this protein at pH 7.2 is: | + | 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] | findSurfaceResiduesListCharged[10.0] | ||
| − | The expected surface charge of this protein at pH 10.0 is: - | + | The expected surface charge of this protein at pH 10.0 is: -14.19 |
| − | |||
| − | |||
| − | |||
</source> | </source> | ||
Revision as of 22:00, 14 March 2023
| 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