Bugs item #3452445, was opened at 2011-12-06 06:38
Message generated for change (Tracker Item Submitted) made by coudert
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Category: Library Functions
Group: 2.3.x
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: François-Xavier Coudert (coudert)
Assigned to: Nobody/Anonymous (nobody)
Summary: fillUC creates duplicate atoms
Initial Comment:
Using "babel --fillUC strict test.cif test.pdb" to transform a structure with a
given symmetry group into a P1 structure creates duplicate atoms. Example with
a "P-1" space group: the atom at (0,0,1/2) is duplicated when symmetry is
removed, leading to two identical atoms at the same position.
$ cat test.cif
data_test
_cell_length_a 10.0000(0)
_cell_length_b 10.0000(0)
_cell_length_c 10.0000(0)
_cell_angle_alpha 90.0000(0)
_cell_angle_beta 90.0000(0)
_cell_angle_gamma 90.0000(0)
_symmetry_space_group_name_H-M 'P -1'
_symmetry_Int_Tables_number 2
_symmetry_cell_setting cubic
loop_
_symmetry_equiv_pos_as_xyz
'+x,+y,+z'
'-x,-y,-z'
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
O1 O 0.0000 0.0000 0.5000
$ babel --fillUC strict test.cif test.pdb
1 molecule converted
1 info messages 21 audit log messages
$ cat test.pdb
COMPND test.cif
AUTHOR GENERATED BY OPEN BABEL 2.3.1
CRYST1 10.000 10.000 10.000 90.00 90.00 90.00 P 1 1
HETATM 1 O HOH 1 -0.000 -0.000 5.000 1.00 0.00 O
HETATM 2 O HOH 2 -0.000 -0.000 5.000 1.00 0.00 O
MASTER 0 0 0 0 0 0 0 0 2 0 2 0
END
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