[cctbxbb] [Dials-support] Issue with hierarchy.as_pdb_string

[Nicholas Sauter]

help is in progress off-list
Nick

Nicholas K. Sauter, Ph. D.
Senior Scientist, Molecular Biophysics & Integrated Bioimaging Division
Lawrence Berkeley National Laboratory
1 Cyclotron Rd., Bldg. 33R0345
Berkeley, CA 94720
(510) 486-5713

On Sat, Apr 28, 2018 at 1:24 AM, Graeme.Winter at Diamond.ac.uk <
Graeme.Winter at diamond.ac.uk> wrote:

> Morning all,
>
> Mike came to the DIALS list with some pdb-reading related issues - however
> in DIALS land we usually don’t mess with this kind of stuff - is there
> someone who can help him out here please?
>
> Many thanks Graeme
>
> On 27 Apr 2018, at 18:14, Wall, Michael E <mewall at lanl.gov<mailto:mewall
> @lanl.gov>> wrote:
>
> Hi,
>
> I'm seeing the following issue with a fresh build of dials development
> source, downloaded within the last hour. There's no error using dials
> v1-9-1. Is this a bug? Something that's being revised right now?
>
> Thanks, Mike
>
> Traceback (most recent call last):
>   File "../../src/xenm_new.py", line 609, in <module>
>     ftmp.write(pdb_in.hierarchy.as_pdb_string(crystal_
> symmetry=pdb_in.input.crystal_symmetry()))
>   File "/home/mewall/packages/dials_devel/modules/cctbx_project/iotbx/pdb/__init__.py",
> line 1191, in crystal_symmetry
>     self_symmetry = self.crystal_symmetry_from_cryst1()
>   File "/home/mewall/packages/dials_devel/modules/cctbx_project/iotbx/pdb/__init__.py",
> line 1168, in crystal_symmetry_from_cryst1
>     return cryst1_interpretation.crystal_symmetry(cryst1_record=line)
>   File "/home/mewall/packages/dials_devel/modules/cctbx_project/
> iotbx/pdb/cryst1_interpretation.py", line 138, in crystal_symmetry
>     unit_cell=u)
>   File "/home/mewall/packages/dials_devel/modules/cctbx_project/
> iotbx/pdb/cryst1_interpretation.py", line 87, in space_group_info
>     try: return sgtbx.space_group_info(self.symbol)
>   File "/home/mewall/packages/dials_devel/modules/cctbx_project/cctbx/sgtbx/__init__.py",
> line 97, in __init__
>     symbols = space_group_symbols(symbol)
> Boost.Python.ArgumentError: Python argument types in
>     space_group_symbols.__init__(space_group_symbols, str)
> did not match C++ signature:
>     __init__(_object*, int space_group_number)
>     __init__(_object*, int space_group_number, std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > extension='')
>     __init__(_object*, int space_group_number, std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > extension='',
> std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> > table_id='')
>     __init__(_object*, std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > symbol)
>
>     __init__(_object*, std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > symbol,
> std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> > table_id='')
>
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