[phenixbb] prepare_pdb_deposition produce incomplete results in version 1.17

[Marta Martinez]

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