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
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