This manual gives you a walk-through on how to use the Major Microspecies Plugin:
The Major Microspecies Plugin determines the major (de)protonated form of the molecule at a specified pH. The output of the plugin is the major microspecies displayed in 2D.
The plugin offers the following options to set in the Major Microspecies Options window:
at pH : sets the pH for the calculation
Take major tautomeric form : if tautomeric forms are more likely to occur, the major one is used to calculate the microspecies.
Fig. 2 Major Microspecies Options window