FindSurfaceCharge: Difference between revisions

From PyMOLWiki
Jump to navigation Jump to search
m (TeddyWarner moved page FindSurfaceResiduesListCharged to FindSurfaceCharge: Significantly changed function)
mNo edit summary
 
(2 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Infobox script-repo
{{Infobox script-repo
|type      = module
|type      = module
|filename  = findSurfaceResiduesListCharged.py
|filename  = findSurfaceCharge.py
|author    = [[User:TeddyWarner|Teddy Warner]]  
|author    = [[User:TeddyWarner|Teddy Warner]]  
|license  = BSD-2-Clause
|license  = BSD-2-Clause
}}
}}


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.
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.
 
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 =


findSurfaceResiduesListCharged [pH=7.0 [, selection=all [, cutoff=2.5 [, doShow=0 ]]]
    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}
* '''selection''' = str: The object or selection for which to find exposed residues {default: all}
* '''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}
* '''doShow''' = 0/1: Change the visualization to highlight the exposed residues vs interior {default: 0}


= Examples =
= Examples =


<gallery>
<gallery>
File:ChargedOutput.PNG|Result of 4FIX.pdb at pH 7.4.
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
fetch 4FIX, async=0
fetch 4FIX


findSurfaceResiduesListCharged
findSurfaceResiduesListCharged


# see how pH changes the protein surface charge:
# see how pH changes the protein surface charge:
findSurfaceResiduesListCharged[7.2]
findSurfaceCharge("4fix",7.0)
     The expected surface charge of this protein at pH 7.2 is: -0.42
    Exposed charged residues:
        ERREDRKEE...
     The expected surface charge of 4fix at pH 7.0 is: +3.24


findSurfaceResiduesListCharged[10.0]
findSurfaceCharge("4fix",7.0,False)
     The expected surface charge of this protein at pH 10.0 is: -13.17
    Charged residues:
        HHHHHHRHERREDRKEE...
     The expected charge of denatured 4fix at pH 7.0 is: +0.13


findSurfaceResiduesListCharged[5.0]
findSurfaceCharge("4fix",10.0)
     The expected surface charge of this protein at pH 5.0 is: +53.02
    Charged residues: ...
     The expected surface charge of 4fix at pH 10.0 is: -3.86


</source>
</source>

Latest revision as of 14:13, 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.

    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

Retrieved from "https://pymolwiki.org/index.php?title=FindSurfaceCharge&oldid=13550"