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

Thank you very much, Billy, for you quick answer. With best wishes, MARTa Billy Poon 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 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

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 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: [email protected]

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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: [email protected]