MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
There are 3 steps how you define the printer dimensions. First define your heat bed. There are already 3 definitions on the right side (MK2, MK2a and custom) and you can also define your own custom data in the free lines between MK2A and custom. Or simply edit the line custom to your needs. After this is done select on the left side under build platform the previously defined heat bed (click in the field and select your choice - your selection was custom, 300x300). The custom build volume define the travel of your extruder nozzle in x, y, z (you data 400x400x500). In this combination it means, that your nozzle is able to travel wider as your heat bed dimensions are (300x300 vs 400x400). This sometimes make sense, e.g. if you need a place to flush a nozzle.
There are different combinations of bed bracket dimensions possible depending on the size of your heat bed and the heat bed platform frame. You can choose one of the predefined bracket versions as long as the line below says "Bracket selection Ok". You need to chose a smaller one in case it shows "Bracket selection not Ok" because this means that there is something wrong with your dimensions for heat bed, heat bed frame and possible bracket mounting holes. The offset is defined by the overlapping heat bed mounting holes and the heat bed frame (see picture on the lower right side).
Hope this will help you.