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Bernhard Rupp wrote:
I run refmac 5.2.0019 on a structure with sequence gaps. Refmac finds those and enters the proper gap links LINK ASN A 34 SER A 37 gap LINK LEU A 67 GLY A 69 gap LINK THR A 125 SER A 127 gap LINK SER A 130 ALA A 132 gap LINK GLY A 189 LYS A 192 gap LINK LYS A 208 LEU A 213 gap LINK SER A 221 GLY A 223 gap LINK ALA A 225 GLN A 227 gap but does not seem to use them, the link distances are all over the place.
Seems to me that is exactly the behavior you would expect with a "gap" link. If you want the the residues connected, shouldn't there be a peptide link? I assume gap link (gap patch?) means deleting the peptide and perhaps adding an OXT to the new C-term. If you delete a few residues because they are not clear in the density, in general the last thing you want is for the residues on either side of the gap to be linked- the peptide bond yanks both chains out of the density and destroys your structure. Ed
