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The question that could be asked here is what is the model supposed to reflect? Should the model be our best guess as to the structure, or what we can and have observed in our electron density maps. In general I think it is better to be conservative and follow the latter. If a non-structural biologist finds what looks like an alanine where they thought a potential lysine for conjugation with a FRET dye should be, then they have another reason to visit the friendly crystallographers down the hall. It also used to be (may still be?) true that SPDBV would build missing atoms (in pink) and warn users of their presence upon loading. Maybe this resolves the issue of how best to build a model without making the coordiates un-friendly for the end user. -bob
