Bugs item #3452445, was opened at 2011-12-06 06:38 Message generated for change (Tracker Item Submitted) made by coudert You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3452445&group_id=40728
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. 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 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3452445&group_id=40728 ------------------------------------------------------------------------------ Cloud Services Checklist: Pricing and Packaging Optimization This white paper is intended to serve as a reference, checklist and point of discussion for anyone considering optimizing the pricing and packaging model of a cloud services business. Read Now! http://www.accelacomm.com/jaw/sfnl/114/51491232/ _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel