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>Try again, but select the 'Reset chain mapping' button (you can get at >that by clicking 'Additional options'). It looks like the old mapping to >the MS1 molecular system is still stored - this way you can reset it. > this didn't work, but... > >This is because you still have a set of constraint lists (or at least >'FixedResonance's that used to belong to them) that are linked to atoms in >the MS1 molSystem - you'll have to delete those. If you start your project >in the FormatConverter, go to Other->General Editor (this will take a >while to set up). > ...I deleted all my constraints lists and was then able to delete MS1. Then I remade my constraints and the export worked fine. thanks, simon