Difference between revisions of "FindSurfaceCharge"

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{{Infobox script-repo
 
{{Infobox script-repo
 
|type      = module
 
|type      = module
−
|filename  = findSurfaceResiduesListCharged.py
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|filename  = findSurfaceCharge.py
 
|author    = [[User:TeddyWarner|Teddy Warner]]  
 
|author    = [[User:TeddyWarner|Teddy Warner]]  
 
|license  = BSD-2-Clause
 
|license  = BSD-2-Clause
 
}}
 
}}
  
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Based on the [[findSurfaceResidues]] script, the [[findSurfaceResiduesListCharged]] script will select and color surface residues and atoms on an object or selection. The function will also identify and output a list of all charged residues on the surface of a selection. This additionally calculates the ionization state of a protein at a given pH.
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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.
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Each time, the script will create two new selections called, '''exposed_res_XYZ''' and '''exposed_atm_XYZ''' where ''XYZ'' is some random number. This is done so that no other selections/objects are overwritten.
 
  
 
= Usage =
 
= Usage =
  
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findSurfaceResiduesListCharged [pH=7.0 [, selection=all [, cutoff=2.5 [, doShow=0 ]]]
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    findSurfaceCharge [selection, [pH, [folded ,[cutoff]]]]
  
 
= Arguments =
 
= 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}
 
* '''pH''' = float: The pH to calculate the surface charge at {default: 7.0}
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* '''selection''' = str: The object or selection for which to find exposed residues {default: all}
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* '''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}
 
* '''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}
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* '''doShow''' = 0/1: Change the visualization to highlight the exposed residues vs interior {default: 0}
 
  
 
= Examples =
 
= Examples =
  
 
<gallery>
 
<gallery>
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Image:ChargedOutput.png|300px|Result of 4FIX.pdb at pH 7.4.
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File:SurfaceCharge.PNG|Result of 4FIX.pdb at pH 7.0.
 
</gallery>
 
</gallery>
  
 
<source lang="python">
 
<source lang="python">
 
run findSurfaceResiduesListCharged.py
 
run findSurfaceResiduesListCharged.py
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fetch 4FIX, async=0
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fetch 4FIX
  
 
findSurfaceResiduesListCharged
 
findSurfaceResiduesListCharged
  
 
# see how pH changes the protein surface charge:
 
# see how pH changes the protein surface charge:
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findSurfaceResiduesListCharged[7.2]
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findSurfaceCharge("4fix",7.0)
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     The expected surface charge of this protein at pH 7.2 is: -0.42
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    Exposed charged residues:
 +
        ERREDRKEE...
 +
     The expected surface charge of 4fix at pH 7.0 is: +3.24
  
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findSurfaceResiduesListCharged[10.0]
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findSurfaceCharge("4fix",7.0,False)
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     The expected surface charge of this protein at pH 10.0 is: -13.17
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    Charged residues:
 +
        HHHHHHRHERREDRKEE...
 +
     The expected charge of denatured 4fix at pH 7.0 is: +0.13
  
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findSurfaceResiduesListCharged[5.0]
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findSurfaceCharge("4fix",10.0)
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     The expected surface charge of this protein at pH 5.0 is: +53.02
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    Charged residues: ...
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     The expected surface charge of 4fix at pH 10.0 is: -3.86
  
 
</source>
 
</source>

Latest revision as of 15:13, 24 March 2023

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

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