Update on this.
It seems that I was wrong, and time spent reading the manual and various
tutorials on PDBx/mmCIF would have yielded dividends. Who would have thought
that (we all know that people write manuals solely for their own benefit ;-))?
However, thanks to all who replied off-board to tell me that the chain ID in
legacy PDB format in _atom_site.auth_asym_id in the mmCIF, and not in either of
the two items I mentioned previously.
best wishes and happy Solstice!
Harry
> On 9 Jun 2023, at 15:57, Harry Powell
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Hi folks
>
> I’ve noticed that for some structures, the PDB file seems to have the mmCIF
> entry for the “_atom_site.label_asym_id” as the chain ID, and for other PDB
> files it has the “_atom_site.label_entity_id”.
>
> e.g. for 4bpq, for ATOM 1 I see -
>
>> CIF: ATOM 1N N . UNK A 1 1 ? 14.187 19.549 -8.010 1.00 0.00 ? 1
>> UNK A N 1
>>
>> PDB: ATOM 1 N UNK A 1 14.187 19.549 -8.010 1.00 0.00
>> N
>>
> but for 6p9o for ATOM 1 I see -
>
>> CIF: ATOM 1 N N . ARG A 1 64 ? -0.538 27.658 131.675 1.00 39.97 ? 64 ARG 1 N
>> 1 64 UNP P03300 643 R
>>
>> PDB: ATOM 1 N ARG 1 64 -0.538 27.658 131.675 1.00 39.97
>> N
>
> both have the corresponding loop items in the same order
>
> loop_
> _atom_site.group_PDB
> _atom_site.id
> _atom_site.type_symbol
> _atom_site.label_atom_id
> _atom_site.label_alt_id
> _atom_site.label_comp_id
> _atom_site.label_asym_id
> _atom_site.label_entity_id
> _atom_site.label_seq_id
>
> so it shouldn’t be that the items are in a different order (which I think is
> allowed in STAR formats).
>
> Any ideas which one is right? Or are they both right? Or both wrong? Or am I
> wrong about this, and have just mis-read the entries? (the refinement program
> for 6p9o is given as both REFMAC and “PHENIX” in the CIF - presumably
> phenix.refine, but I wouldn’t bet my house on it).
>
> Harry
>
>
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing
> list hosted by www.jiscmail.ac.uk, terms & conditions are available at
> https://www.jiscmail.ac.uk/policyandsecurity/
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
