Thank you Robbie. I guess ligands do not (or should not) appear in SEQRES therefore should not have a TER record.
Eleanor On 19 June 2017 at 11:04, Robbie Joosten <robbie_joos...@hotmail.com> wrote: > Hi Eleanor, > > From PDB format 3.3: > * Every chain of ATOM/HETATM records presented on SEQRES records is > terminated with a TER record. > * The TER records occur in the coordinate section of the entry, and > indicate the last residue presented for each polypeptide and/or nucleic > acid chain for which there are determined coordinates. For proteins, the > residue defined on the TER record is the carboxy-terminal residue; for > nucleic acids it is the 3'-terminal residue. > * For a cyclic molecule, the choice of termini is arbitrary. > * Terminal oxygen atoms are presented as OXT for proteins, and as O5’ or > OP3 for nucleic acids. These atoms are present only if the last residue in > the polymer is truly the last residue in the SEQRES. > * The TER record has the same residue name, chain identifier, sequence > number and insertion code as the terminal residue. The serial number of the > TER record is one number greater than the serial number of the ATOM/HETATM > preceding the TER. > > It seems that many programs are indeed overenthusiastic and also putting > them behind non-polymer residues or carbohydrates. TER records also appear > (IMO incorrectly) after linker residues that are in SEQRES, but are not > amino acids. This indeed causes side effects. I also noticed that COOT > leaves TER records if you add C-terminal residues. This can cause Refmac to > think that the residues should not be connected. > > Cheers, > Robbie > > > > -----Original Message----- > > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > > Eleanor Dodson > > Sent: Monday, June 19, 2017 11:42 > > To: CCP4BB@JISCMAIL.AC.UK > > Subject: [ccp4bb] REFMAC? COOT? and TER records > > > > These do seem to multiply wonderfully in the PDB output files and > > sometimees to have have strange effects/ affects in COOT? > > > > > > As I understand there should be a TER record after a protein chain? but > not > > after a ligand. > > > > > > Dont know about carbohydrate chains. > > > > > > Eleanor > > > > > > The correspondence about N linked glycosylation brought it up.. > > > > > > > > > > > > > >
