Re: [ccp4bb] REFMAC? COOT? and TER records

[Eleanor Dodson]

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  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..
> >
> >
> >
> >
> >
> >
>
>

Re: [ccp4bb] REFMAC? COOT? and TER records

[Robbie Joosten]

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..
> 
> 
> 
> 
> 
>