How to manually clear OC1A and OC1B?
It is possible to configure the timer to to toggle OC1A with

TCCR1A |= (1 &lt;&lt; COM1A0);


Within the interrupt routine use the control register to trigger an additional compare event. This does NOT have side effects like changing the timer value.

TCCR1C |= (1 &lt;&lt; FOC1A);


To change immediatly set the type to clear or set mode and trigger a change

TCCR1A = (1 &lt;&lt; COM1A0);
TCCR1C |= (1 &lt;&lt; FOC1A);


see https://www.sparkfun.com/datasheets/Components/SMD/ATMega328.pdf p.137