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

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, [email protected] < [email protected]> 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 > 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 extension='') __init__(_object*, int space_group_number, std::__cxx11::basic_string extension='', std::__cxx11::basic_string table_id='') __init__(_object*, std::__cxx11::basic_string symbol)

__init__(_object*, std::__cxx11::basic_string symbol, std::__cxx11::basic_string table_id='')

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