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 >> > >> >
