--
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


---------- Forwarded message ---------
From: Billy Poon <BKPoon@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@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


On Mon, Mar 9, 2020 at 10:05 AM Marta Martinez <mmmtnez@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@cnb.csic.es

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