Chain(s) and Parameter Area

 

 

Electrostatic Potential
[ ref. ]

 

Electrostatic Potential is calculated using Delphi (12) program according to the modifications done by Walter Rocchia (13) and further adapted to JPD requirements (to be published).


Placing the cursor above this element: pop-up area will show the position (sequence number and AA three letter code) for selected amino acid and the 4 numerical values for EP (@Calpha, @Last Heavy Atom (LHA), @Surface patch closest to the selected residue and Average EP) for this amino acid.
Left mouse click: no action
Right mouse click: on any of the "EP" will generate following menu and actions:





A) STING it "EP @Calpha": This option generates structural presentation with color coding of the amino acids corresponding to the "EP" color coding. Amino acids are presented in CPK rendering. EP at the alpha carbon is presented.



B) STING it "EP @LHA": This option generates structural presentation with color coding of the amino acids corresponding to the "EP" color coding. Amino acids are presented in CPK rendering. EP at the Last Heavy Atom of the side chain is presented.



C) STING it "EP @Surface": This option generates structural presentation with color coding of the amino acids corresponding to the "EP" color coding. Amino acids are presented in CPK rendering. EP at the Surface patch closest to the selected amino acid is presented.



D) STING it "EP Average": This option generates structural presentation with color coding of the amino acids corresponding to the "EP" color coding. Amino acids are presented in CPK rendering. The average of EP values taken from all atoms of the selected amino acid is presented.


E) The EP values shown at the picture below, were generated using GRASP program. We use Delphi program from same lab (Barry Hong's lab - Columbia University, NYC-USA). Figure below shows the difference in concept when data display is in question: GRASP does it one parameter at the time shown at the molecular surface. BLUE STAR STING JPD does it all parameters at the same time for all amino acids (including those at the surface).