Новосибирский институт органической химии им. Н.Н. Ворожцова СО РАН

Лаборатория изучения механизмов органических реакций


Usage: cif2xyz [options] *.cif

Dependencies: perl

Convert cif to MDL xyz format (filename.cif to filename.xyz)
The program prints filename to sdtout and warns (to stderr) if fractional
coordinates block of cif-file contains not exactly one molecule.

-cell=MxNxK  fill unit cell by symmetry operations and then
             multiply the cell M,N,K times by a,b,c directions
             (initial unit cell places in the centre of supercell)
-cell=N      equal -cell=NxNxN
-cell        equal -cell=1x1x1 (only pack unit cell)
-move_to_cell_center  move molecules included in unit cell to the cell center  
-exclude_initial      f.e. for -cell=3x3x3 make 26 unit cells (without central)
-cell_corners         add dummies XX in the unit cell corners
-all_inside_cell  place all atoms given in cif-file inside the unit cell
                  (as obabel does, not a whole molecule is obtained).
                  This option is too little tested.

   The program takes fractional coordinates 'as is' without trying to grow
molecules or eliminate disorder. So, it doesn't operate correctly with the 
symmetric molecules (not a whole molecules are obtained). A sign of disorder 
or not-a-whole-molecule is warning 'Formulas are not coincided' (however, 
occasionally this warning is caused by an error in _chemical_formula_sum).

Последняя модификация: Thu Aug 9 10:29:29 2018