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

[Billy Poon]

--
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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