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, herman.schreu...@sanofi.com <herman.schreu...@sanofi.com> 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:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von > Eleanor Dodson > Gesendet: Dienstag, 7. November 2017 13:28 > An: CCP4BB@JISCMAIL.AC.UK > 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 > <rendezvous.a...@gmail.com<mailto:rendezvous.a...@gmail.com>> 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 > <eleanor.dod...@york.ac.uk<mailto:eleanor.dod...@york.ac.uk>> 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 >> <rendezvous.a...@gmail.com<mailto:rendezvous.a...@gmail.com>> >> 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 >>> <agg.rash...@gmail.com<mailto:agg.rash...@gmail.com>> 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 >>> > >>> >> > >
