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Spacecraft commanding requires attention to minute detail, because any mistake could end the mission. This issue is compounded by the great distance between Mercury and Earth: a wrong command could put MESSENGER’s sunshade in the wrong direction, overheating critical spacecraft systems before the ground operations crew could learn of the problem, much less intervene. All of MESSENGER’s commands must thus be carefully designed, checked, and double-checked, and then transmitted to the spacecraft for storage in the onboard processors for later execution. And while the spacecraft must be protected, there is a long menu of scientific observations that must be completed to meet mission requirements, some keyed to particular combinations of locations and lighting conditions. Resources on the spacecraft must also be considered, including the maximum number of storable commands, the capacity of the solid-state recorder to store data prior to downlink, times of downlink windows, and data rates. To deal with all of these requirements, as well as to re-plan operations rapidly in the event of mission anomalies, a science planning software tool was developed to plan MESSENGER science acquisition sequences. This software tool, SciBox, had been used previously to help with planning individual instrument sequences on other missions, in particular the Magnetospheric Imaging Instrument on Cassini and the Compact Reconnaissance Imaging Spectrometer for Mars on the Mars Reconnaissance Orbiter, but the first use of SciBox for planning, optimizing, and generating command sequences for observations with a multiple-instrument payload on a full mission has been with MESSENGER. SciBox takes mission parameters, observation requirements, and individual instrument commands and generates command-sequence loads that can then be uploaded for execution on the spacecraft. By minimizing the person-in-the-loop portion of sequence development, observations can be optimized and rapidly implemented for the full instrument suite. Above, we see an animation showing spacecraft attitude adjustments (accelerated) as commanded by SciBox in support of science operations.