[phenixbb] uniq segid problem

[Oleg Sobolev]

Hi jpd,

The error means that you have the same atoms in the model, i.e. same atom
name, chain name, residue name, residue number, segment id. It might not be
the case and something for us to fix, especially if it was not like this in
the previous version. Can you please share the model (off-list) or small
part of the model which still produces the error so I can investigate? The
model will be treated confidentially.

Best regards,
Oleg Sobolev.

On Wed, Mar 6, 2024 at 1:17 PM jp d <yoyoq at yahoo.com> wrote:

> hi,
> phenix is crashing with "segid is not unique" problems
>
> i have an old job that ran fine in 1.20,
> in 1.21-5207 i get this (same job script)
>
> Sorry: residue.id_str(suppress_segid=false): segid is not unique:
>   pdbres="ALA    65 " segid="PPP "
>
>
> i think the appropriate place in the log is this:
>
>    Chain: " "
>       Number of atoms: 41993
>       Number of conformers: 1
>       Conformer: ""
>         Number of residues, atoms: 1519, 32612
>           Duplicate atoms: {'  A,C1*': 112, '  A,C2': 112, '  A,C2*': 112,
> '  A,C3*': 112, '  A,C4': 112, '  A,C4*': 112, '  A,
> C5': 112, '  A,C5*': 112, '  A,C6': 112, '  A,C8': 112, '  A,N1': 112, '
> A,N3': 112, '  A,N6': 112, '  A,N7': 112, '  A,N9': 1
> 12, '  A,O1P': 112, '  A,O2*': 112, '  A,O2P': 112, '  A,O3*': 112, '
> A,O4*': 112, '  A,O5*': 112, '  A,P': 112, '  C,C1*': 71
> , '  C,C2': 71, '  C,C2*': 71, '  C,C3*': 71, '  C,C4': 71, '  C,C4*': 71,
> '  C,C5': 71, '  C,C5*': 71, '  C,C6': 71, '  C,N1':
>  71, '  C,N3': 71, '  C,N4': 71, '  C,O1P': 71, '  C,O2': 71, '  C,O2*':
> 71, '  C,O2P': 71, '  C,O3*': 71, '  C,O4*': 71, '  C,
> O5*': 71, '  C,P': 71, '  G,C1*': 179, '  G,C2': 179, '  G,C2*': 179, '
> G,C3*': 179, '  G,C4': 179, '  G,C4*': 179, '  G,C5':
> 179, '  G,C5*': 179, '  G,C6': 179, '  G,C8': 179, '  G,N1': 179, '
> G,N2': 179, '  G,N3': 179, '  G,N7': 179, '  G,N9': 179, '
>   G,O1P': 179, '  G,O2*': 179, '  G,O2P': 179, '  G,O3*': 179, '  G,O4*':
> 179, '  G,O5*': 179, '  G,O6': 179, '  G,P': 179, '
> U,C1*': 69, '  U,C2': 69, '  U,C2*': 69, '  U,C3*': 69, '  U,C4': 69, '
> U,C4*': 69, '  U,C5': 69, '  U,C5*': 69, '  U,C6': 69,
>  '  U,N1': 69, '  U,N3': 69, '  U,O1P': 69, '  U,O2': 69, '  U,O2*': 69,
> '  U,O2P': 69, '  U,O3*': 69, '  U,O4': 69, '  U,O4*':
>  69, '  U,O5*': 69, '  U,P': 69}
>        Classifications: {'RNA': 1519}
>        Modifications used: {'rna2p': 1, 'rna2p_pur': 82, 'rna2p_pyr': 63,
> 'rna3p': 10, 'rna3p_pur': 497, 'rna3p_pyr': 444}
>        Link IDs: {'rna2p': 146, 'rna3p': 1372}
>
>
> the 1.20 log does not have these messages and finished normally.
> maybe a wildcard problem with those stars ?
>
> we are not using the '*' in our files
> has anyone seen that ? should i go back to 1.20 ?
> or force it to use the 1.20 chem data lib ?
>
> thanks
> jpd
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