If you output an mmCIF file directly from refmac this avoids the TER
record problem.
just add this
"pdbout format mmcif"
to your refmac command and it will output an mmCIF which can be used
directly for deposition to the PDB
see https://www.wwpdb.org/deposition/preparing-pdbx-mmcif-files
Regards
John
PDBe
On 07/11/2017 15:02, Bernhard Rupp wrote:
> This TER business is a common lament generally surfacing upon deposition.
> PDB demands TER only after a peptide chain, but refmac inserts
> them liberally after HETATM chains and in between them if the HET
> monomers are not consecutively numbered.
>
> Example:
> .
> HETATM 4626 C8 NAG A 652 -7.708 54.612 47.885 1.00 66.94 C
> HETATM 4627 O7 NAG A 652 -6.870 54.052 45.727 1.00 74.93 O
> TER 4628 NAG A 652
> HETATM 4629 CL CL A 801 21.660 57.665 44.396 1.00 72.44 CL
> HETATM 4630 CL CL A 802 9.893 42.272 48.748 1.00 44.08 CL
> TER 4631 CL A 802
> ATOM 4632 N PHE B 11 24.376 -12.877 29.777 1.00 80.09 N
> ATOM 4633 CA PHE B 11 24.701 -14.037 28.894 1.00 80.63 C
> .
> I have a crude hack removes aberrant TERs but it is
> in F90 and no guarantees whatsoever case someone wants it.
>
> Best, BR
>
> -----Original Message-----
> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Marcin Wojdyr
> Sent: Tuesday, November 7, 2017 5:33 AM
> To: [log in to unmask]
> Subject: Re: [ccp4bb] Removing a ter line present in the middle of the chain
>
> On 7 November 2017 at 12:28, Eleanor Dodson <[log in to unmask]> wrote:
>> Something (Refmac? Coot?? mystery?) was labelling all atoms in MSE
>> residues as HETATM and that was a BAD THING..
> I don't dispute this, but that's what the pdb spec from the PDB requires (HETATM for all non-standard residues).
> Example: https://files.rcsb.org/view/5ABS.pdb
>
> Marcin
--
John Berrisford
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492529
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