I am using Open Babel 2.3.1 on OsX and Windows and have various errors
converting a cif file CIF to XYZ.
Convert is done properly on OsX command line but fails in Windows
commandline or program call OsX
Advices or comments are welcome
Thanks in advance
-----------------
Command line : obabel "obabel RbLaF4_Short.cif oxyz"
OsX command line :
conversion is done properly
Windows commandline :
C:\Users\massiot.CEMHTI\Dropbox\EXAVIZ\CIF Simple Examples>obabel
RbLaF4_Short.c
if -oxyz
==============================
*** Open Babel Warning in OpenBabel::OBGlobalDataBase::Init
Unable to open data file 'space-groups.txt'
==============================
*** Open Babel Warning in OpenBabel::OBGlobalDataBase::Init
Cannot initialize database
==============================
*** Open Babel Warning in OpenBabel::SpaceGroup::Find
Unknown space group (HM:,Hall:) with incomplete or wrong definition.
==============================
*** Open Babel Warning in OpenBabel::CIFData::ExtractSpacegroup
CIF Error: missing spacegroup description: defaulting to P1... (in data
block:
)
OsX C++ program (runs properly for CML /SDF conversion
Reads no molecules
/Users/dominiquemassiot/Dropbox/EXAVIZ/OpenBabelCommandLine/build/Debug/Open
BabelCommandLine
Test with link to OpenBabel
---------------------------
Usage: ProgrameName InputFileName OutputFileName
use default values for test
Input file '/Users/dominiquemassiot/Dropbox/EXAVIZ/CIF Simple
Examples/RbLaF4_Short.cif'
Output file '/Users/dominiquemassiot/Dropbox/EXAVIZ/CIF Simple
Examples/RbLaF4_Short.xyz'
==============================
*** Open Babel Warning in ReadMolecule
Problems reading a CIF file: no structure found !
0 molecules converted
end
Following is the CIF input file (very basic) RbLaF4_Short.cif
------------------
# from //Crmht_10/Users/Mathieu ALLIX/1-Collaborations/ALR/LaRbF4/Publi
LaRbF4/Affinement Publi/FINAL_COMBINED_WEIGHING250_TTANISO.EXP
_audit_creation_date 2010-11-30T09:39:12
_symmetry_space_group_name_H-M 'P n m a'
_cell_length_a 6.462812
_cell_length_b 3.864979
_cell_length_c 16.176291
_cell_angle_alpha 90.0000
_cell_angle_beta 90.0000
_cell_angle_gamma 90.0000
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_B_iso_or_equiv
_atom_site_occupancy
Rb RB+1 0.27509 0.75000 0.20070 0.713768584496 1.00000
La1 LA+3 0.25179 0.25000 0.44119 0.535326438372 1.00000
F1 F-1 0.13392 0.25000 0.03695 0.646892258051 1.00000
F2 F-1 0.00067 0.75000 0.44397 0.706741438034 1.00000
F3 F-1 0.39137 0.75000 0.36973 1.17724442421 1.00000
F4 F-1 0.09340 0.25000 0.31114 1.19564133573 1.00000
------------------
---------------------------------------------------------------------
Dominique Massiot
e-mail : dominique.mass...@cnrs-orleans.fr
<mailto:dominique.mass...@cnrs-orleans.fr>
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