[phenixbb] single atom mmcif bug

[Oleg Sobolev]

Dear Edwin,

Thank you for pointing it out!

It was oversight in procedure for creating internal model representation
from mmCIF files in cctbx library. I'm happy to report that this has been
fixed and newer versions of Phenix (after 3254) and cctbx library should
behave as expected.

Cctbx uses its own tools to parse mmCIF, so I don't know if this
corner-case could be an issue for other libraries/software.

Best regards,
Oleg Sobolev.


On Wed, Sep 5, 2018 at 1:35 PM, Edwin Pozharski <pozharskibb at gmail.com>
wrote:

> There appears to be a bug in phenix.cif_as_pdb. I am looking at a bunch of
> files that contain very few atoms.  When it's more than one, mmcif contains
> multiple HETATM records in a loop.  However,  single atom entries seem to
> encode atomic coordinates in a different way, like so
>
> #
> _atom_site.group_PDB             HETATM
> _atom_site.id                    4905
> _atom_site.type_symbol           CA
> _atom_site.label_atom_id         CA
> _atom_site.label_alt_id          .
> _atom_site.label_comp_id         CA
> _atom_site.label_asym_id         L
> _atom_site.label_entity_id 5
> _atom_site.label_seq_id          .
> _atom_site.pdbx_PDB_ins_code     .
> _atom_site.Cartn_x               0.394
> _atom_site.Cartn_y               -6.965
> _atom_site.Cartn_z               18.775
> _atom_site.occupancy             1
> _atom_site.B_iso_or_equiv        2
> _atom_site.pdbx_formal_charge    ?
> _atom_site.auth_atom_id          CA
> _atom_site.auth_comp_id          CA
> _atom_site.auth_asym_id          A
> _atom_site.auth_seq_id           701
> _atom_site.pdbx_PDB_model_num    1
>
> This does not include _loop statement and instead lists parameters
> directly.  If I try to convert this to pdb, cif_as_pdb fails like so (and I
> suspect that pretty much any cif-file read would fail)
>
>   Python argument types in
>     double.__init__(double, str)
> did not match C++ signature:
>     __init__(boost::python::api::object, boost::python::numeric::array)
>     __init__(boost::python::api::object, boost::python::tuple)
>     __init__(boost::python::api::object, boost::python::list)
>     __init__(boost::python::api::object, std::vector<double,
> std::allocator<double> >)
>     __init__(boost::python::api::object, scitbx::af::const_ref<std::string,
> scitbx::af::trivial_accessor>)
>     __init__(_object*, scitbx::af::shared_plain<double>)
>     __init__(_object*, unsigned long)
>     __init__(_object*, unsigned long, double)
>     __init__(_object*, scitbx::af::flex_grid<scitbx::af::small<long,
> 10ul> >)
>     __init__(_object*, scitbx::af::flex_grid<scitbx::af::small<long,
> 10ul> >, double)
>     __init__(_object*)
>
> This has nothing to do with how many atoms are there, obviously - in fact,
> removing all HETATM records but one from a cif file that has _loop
> statement does not produce this bug.
>
> The obvious guess is that the bug is somewhere in mmdb (I am assuming here
> that phenix relies on it for cif read/write).
>
> This is not a big deal, of course - in most scenarios, a structure
> contains more than one atom.  It does not interfere with me either - I am
> discarding single atom cases in this analysis anyway (so it is actually
> serves as an unintentional filter).
>
> Still, it looks like a bug.  I am not an expert in mmcif format, but iiuc,
> there is no strict requirement for atom_site category to have a _loop.  If
> there is (I can't find any such syntax requirement), then the source of the
> data files (PDBe coordinate server) would be at fault for not structuring
> the data properly.
>
> Cheers,
>
> Ed.
>
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