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> Seems to me that is exactly the behavior you would expect with a "gap" link. No, perhaps misunderstanding. This is a contiguous chain, just numbered discontinuously according to some biological reason. So the distances are very close to correct peptide links, and refmac in fact calls the link a 'GAP LINK' (<-term LINK!) so it seems to have properly identified them as close enough together? > If you delete a few residues because they are not clear in the density, Correct, but that would be obvious from improbable distances? Maybe there is no check or cutoff for that situation in the program. PS: Sorry for the bad line breaks in my email re corrected LINK entry. TRANS starts right above gap. br
