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Hi Christoph, > Thank you for the help. Now I know what I have to do next time. Wouldn't > it be better if one could choose the resonances that are used for > linking explicitly instead of choosing the format? I didn't expect for > example that the program still knows that the other resonance list was > once imported from Sparky. The problem is that different file formats tend to have different naming systems for their atoms, and you would have to do a lot of manual Resonance->Atom assignments while running linkResonances when you mix the atom names originating from different formats (as opposed to using the naming system that best fits one particular format at a time). In any case, for linkResonance purposes, it's best to keep the Resonances grouped by their original import format. You can rerun linkResonances several times if you imported data from different formats. Explicitly choosing resonances is not really a good option, as you would quickly end up with over 1000 for a normal-sized protein. Wim