Douglas Kojetin asked the following question on February 9, 2005: >For example, the molecular surface "numbers" default to >-1, 0 and 1. If they are changed to -5, 0 and 5, the displayed surface >looks "less charged" than that displayed with the default numbers. >What do the numbers mean?
I'm not an expert on this, but the eletrostatic potential at the surface is often expressed in kT/e and that is also the unit listed in the header of the .dx file created by APBS. So my guess is that the numbers represent kT/e. When the surface potentials are displayed in PyMOL a linear interpolation is used to display the colors (completely red at or below -1 kT/e and completely blue at or above +1 kT/e). If you change the numbers from -1,0,+1 to -5,0,+1 an eletrostatic potential of -1 kT/e will no longer be completely red but instead somewhere inbetween red and white and that is why your protein will *look* less charged (the actuaæ potentials are of course identical, it is only their representation that is changed). Other factors that are likely to affect the electrostatic potential are the dielectric constants of the molecule (protein) and solvent, the temperature (298.15 K for a somewhat high "room-temperature" of 25'C, 310.15 K for human body temperature of 37'C) and the ionic strength. All these parameters can be set in the APBS tools plugin or directly in the APBS input (.in) file. Kind Regards, ./ Kristoffer
