[phenixbb] Fwd: prepare_pdb_deposition produce incomplete results in version 1.17

[Marta Martinez]

Thank you very much, Billy, for you quick answer.

With best wishes,

MARTa


Billy Poon <BKPoon at lbl.gov> escribió:

> --
> Billy K. Poon
> Research Scientist, Molecular Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> 1 Cyclotron Road, M/S 33R0345
> Berkeley, CA 94720
> Tel: (510) 486-5709
> Fax: (510) 486-5909
> Web: https://phenix-online.org
>
>
> ---------- Forwarded message ---------
> From: Billy Poon <BKPoon at lbl.gov>
> Date: Wed, Mar 11, 2020 at 11:51 PM
> Subject: Re: [phenixbb] prepare_pdb_deposition produce incomplete results
> in version 1.17
> To: Marta Martinez <mmmtnez at cnb.csic.es>
>
>
> Hi Marta,
>
> The mmCIF functionality is very much still a work in progress as we try to
> make the process more robust. The ? in the column from 1.17 is a
> consequence of some changes we had made to the code and we're working on
> fixing that. The secondary structure issue with Chimera is separate since
> that column is for matching the protein chain with the sequence, not as a
> way to annotate secondary structure. We are working with the wwPDB to make
> sure our output is in compliance with the latest mmCIF dictionary.
>
> Let us know if you have any other questions. Thanks!
>
> --
> Billy K. Poon
> Research Scientist, Molecular Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> 1 Cyclotron Road, M/S 33R0345
> Berkeley, CA 94720
> Tel: (510) 486-5709
> Fax: (510) 486-5909
> Web: https://phenix-online.org
>
>
> On Mon, Mar 9, 2020 at 10:05 AM Marta Martinez <mmmtnez at cnb.csic.es> wrote:
>
>>
>> Hi,
>>
>>    In the past (phenix version 1.13) we have been using
>> prepare_pdb_deposition to generate  CIF files of atomic structures. In
>> the last version (1.17) the program produces an incomplete output if
>> the input is a PDB file.
>>
>>     The tests have been carried out with the protein hemoglobin (PDB
>> ID = 5ni1). If we downloaded it from the PDB databank we get the file
>> 5ni1.cif. If we "export" 5ci1.cif using prepare_pdb_deposition the
>> result is correct. On the other hand, if we convert 5ci1.cif  to PDB
>> either using chimera uscf or maxit
>> (https://sw-tools.rcsb.org/apps/MAXIT/index.html) and then we execute
>> prepare_pdb_deposition, one of the columns (label name =
>> _atom_site.label_entity_id) is filled with the symbol "?" instead of
>> the label_entity_id (as the version 1.13 did). One of the effects of
>> this misbehavior is that chimera displays the file as a set of
>> aminoacids with no connection between them (no secondary structure is
>> shown)
>>
>>
>>
>> A few lines of the file obtained using phenix 1.17:
>>
>>     ATOM 1 N . VAL A 1 ? 45.71600 55.72700 67.16700 1.000 80.64000 N ? A ?
>> 1 1
>>     ATOM 2 CA . VAL A 1 ? 46.41500 54.48900 67.60900 1.000 80.57000 C ? A
>> ? 1 1
>>     ATOM 3 C . VAL A 1 ? 45.42800 53.30800 67.68900 1.000 75.67000 C ? A ?
>> 1 1
>>
>> Corresponding lines of the equivalent file obtained using phenix 1.13
>>
>>     ATOM 1 N . VAL A 1 ? 45.71600 55.72700 67.16700 1.000 80.64000 N ? A 1
>> 1 1
>>     ATOM 2 CA . VAL A 1 ? 46.41500 54.48900 67.60900 1.000 80.57000 C ? A
>> 1 1 1
>>     ATOM 3 C . VAL A 1 ? 45.42800 53.30800 67.68900 1.000 75.67000 C ? A 1
>> 1 1
>>
>> Note the difference in the ante-penultimate column.
>>
>> We would appreciate if phenix 1.17 is modified so the column
>> _atom_site.label_entity_id is filled with the proper chain ID.
>>
>>     best wishes
>>
>> --
>> Marta Martinez Gonzalez
>>
>> Biocomputing Unit (Lab B13)
>> National Center for Biotechnology-CSIC
>> Darwin, 3. Campus de la Universidad Autonoma de Madrid
>> 28049 Madrid. Spain
>> Tel:+34 915854510 Fax:+34 913720112
>> E-mail: mmmtnez at cnb.csic.es
>>
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>>


-- 
Marta Martinez Gonzalez

Biocomputing Unit (Lab B13)
National Center for Biotechnology-CSIC
Darwin, 3. Campus de la Universidad Autonoma de Madrid
28049 Madrid. Spain
Tel:+34 915854510 Fax:+34 913720112
E-mail: mmmtnez at cnb.csic.es