define ~oxyA (oxygen and ~chainA) define ~oxyB (oxygen and ~chainB) define ~hydA (hydrogen and ~chainA and not within(1.2,carbon)) define ~hydB (hydrogen and ~chainB and not within(1.2,carbon)) select all connect 1.2 2.5 (~oxyA) (~hydB) hbond create connect 1.2 2.5 (~oxyB) (~hydA) hbond create hbonds on hbonds 0.2 color hbonds [xccccff] # MW polar color