Any non-0standard amino acid should be labelled l-peptide I think.. TYC is labelled like this: ir NOT as a L-peptide so REFMAC is probably sensible to believe a TER card is required..
chem_comp.desc_level TYC TYC 'L-TYROSINAMIDE ' non-polymer 25 13 . On 7 November 2017 at 15:30, Abhishek Anan <[email protected]> wrote: > I had a similar issue with refmac inserting TER card after some but > not all HETATM. It was inserting them before TYC (amidated tyrosine) > but not before norleucine or some of the other non-natural amino acids > I had. It might have something to do with the cif file and not > something particular to HETATM. Just a thought! > > Abhishek > > On 11/7/17, [email protected] <[email protected]> > wrote: > > My feeling is that all non-standard amino acids should be labeled HETATM > and > > that the overzealous introduction of TER cards by Refmac is the bad > thing, > > but I might be mistaken… > > Herman > > > > Von: CCP4 bulletin board [mailto:[email protected]] Im Auftrag von > > Eleanor Dodson > > Gesendet: Dienstag, 7. November 2017 13:28 > > An: [email protected] > > Betreff: [EXTERNAL] Re: [ccp4bb] Removing a ter line present in the > middle > > of the chain > > > > Well - I just edited the HETATM to ATOM and the TER went away.. > > Something (Refmac? Coot?? mystery?) was labelling all atoms in MSE > residues > > as HETATM and that was a BAD THING.. > > Eleanor > > > > > > On 7 November 2017 at 08:05, Abhishek Anan > > <[email protected]<mailto:[email protected]>> wrote: > > Are you LINK records properly defined? You might want to check them. I > > had a similar issue and updating links fixed it. > > > > Best > > Abhishek > > > > On 11/7/17, Eleanor Dodson > > <[email protected]<mailto:[email protected]>> wrote: > >> No - it is not. > >> > >> I have seen similar problems. > >> Your atom records arent labelled as HETATM are they? > >> > >> That triggers strange behavior. > >> Eleanor > >> > >> > >> On 7 November 2017 at 07:13, Abhishek Anan > >> <[email protected]<mailto:[email protected]>> > >> wrote: > >> > >>> Are you adding the cif file of the unnatural amino acid on LIB in path > >>> in refmac. > >>> > >>> Best, > >>> Abhishek > >>> > >>> > >>> > >>> On 11/7/17, Rashi Aggarwal > >>> <[email protected]<mailto:[email protected]>> wrote: > >>> > Dear all, > >>> > > >>> > I have an unnatural amino acid in my structure which I could > >>> > successfully > >>> > add in coot. The amino acid is taking the right bonds when viewed > with > >>> > coot. However, the pdb file has a ter line just above the residue. > >>> > > >>> > If I remove this line and submit the pdb to refmac it again adds the > >>> > ter > >>> > line, I can still remove it and go ahead with validation but is it > the > >>> > right thing to do? > >>> > > >>> > Thanks > >>> > > >>> > Best, > >>> > Rashi > >>> > > >>> > >> > > > > >
