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This TER business is a common lament generally surfacing upon deposition. PDB demands TER only after a peptide chain, but refmac inserts them liberally after HETATM chains and in between them if the HET monomers are not consecutively numbered. Example: . HETATM 4626 C8 NAG A 652 -7.708 54.612 47.885 1.00 66.94 C HETATM 4627 O7 NAG A 652 -6.870 54.052 45.727 1.00 74.93 O TER 4628 NAG A 652 HETATM 4629 CL CL A 801 21.660 57.665 44.396 1.00 72.44 CL HETATM 4630 CL CL A 802 9.893 42.272 48.748 1.00 44.08 CL TER 4631 CL A 802 ATOM 4632 N PHE B 11 24.376 -12.877 29.777 1.00 80.09 N ATOM 4633 CA PHE B 11 24.701 -14.037 28.894 1.00 80.63 C . I have a crude hack removes aberrant TERs but it is in F90 and no guarantees whatsoever case someone wants it. Best, BR -----Original Message----- From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Marcin Wojdyr Sent: Tuesday, November 7, 2017 5:33 AM To: [log in to unmask] Subject: Re: [ccp4bb] Removing a ter line present in the middle of the chain On 7 November 2017 at 12:28, Eleanor Dodson <[log in to unmask]> wrote: > > Something (Refmac? Coot?? mystery?) was labelling all atoms in MSE > residues as HETATM and that was a BAD THING.. I don't dispute this, but that's what the pdb spec from the PDB requires (HETATM for all non-standard residues). Example: https://files.rcsb.org/view/5ABS.pdb Marcin