NONSYM

SYMMETRY TOOLS

PLATON HOMEPAGE

Search for and analysis of non-crystallographic symmetry

A search for non-crystallographic symmetry in a structural model is done on two levels

1. Intra-molecular

   The point group symmetry of isolated molecules (residues) is determined following the SYMMOL algorithm of T. Pilati & A. Forni, J.Appl.Cryst. (1998), 31, 503-504.

   Examples:

   bucky.spf gives pointgroup Ih for C60.

   c476.spf gives pointgroup Td for C476.

   Note:

   • Hydrogen atoms are left out of the analysis.

   • The analysis is done for each discrete residue, starting with a distance tolerance of 0.1 and stepping up by 0.1 up to 0.8 until symmetry is detected.

   • The starting point of the tolerance can be given optionally on the keyboard instruction.

   Example: CALC NONSYM 0.5

   ---

   Sample output of NONSYM/SYMMOL for cubane (space group R-3, site symm -3).

   
   ================================================================================
   SYMMOL: Search for (additional) Molecular Symmetry
   ================================================================================
   
   Molecular Symmetry see: T. Pilati & A. Forni, J.Appl.Cryst. (1998), 31, 503-504
   For CSM, see: H. Zabrodsky et al. (1993) JACS, 115, 8278-8298
   
   ================================================================================
   Resd #         Inertial  Moments    Degree Symbol    CSM           RMS    Tol
   --------------------------------------------------------------------------------
       1      116.      116.      115.    3   Oh       0.0105        0.0102 0.10
   
    Symmetry element     CSM and Max.Diff.  Symmetry element     CSM and Max.Diff. 
     1 [E  ] x,y,z           0.0000 0.0000   2 [C3 ] y,z,x           0.0042 0.0080 
     3 [C2 ] -x,-y,z         0.0063 0.0086   4 [C4 ] x,z,-y          0.0105 0.0144 
     5 [C2 ] x,-y,-z         0.0084 0.0130   6 [C2 ] -x,y,-z         0.0063 0.0086 
     7 [Cs ] x,y,-z          0.0063 0.0086   8 [Ci ] -x,-y,-z        0.0000 0.0000 
     9 [C3 ] z,x,y           0.0042 0.0080  10 [C3 ] -y,z,-x         0.0098 0.0125 
    11 [C2 ] z,-y,x          0.0073 0.0106  12 [C3 ] -y,-z,x         0.0070 0.0121 
    13 [C3 ] y,-z,-x         0.0070 0.0121  14 [S6 ] y,-z,x          0.0098 0.0125 
    15 [S6 ] -y,-z,-x        0.0042 0.0080  16 [C3 ] z,-x,-y         0.0070 0.0121 
    17 [C4 ] -y,x,z          0.0084 0.0129  18 [C3 ] -z,x,-y         0.0070 0.0121 
    19 [C3 ] -z,-x,y         0.0098 0.0125  20 [S6 ] -z,x,y          0.0070 0.0121 
    21 [S6 ] -z,-x,-y        0.0042 0.0080  22 [C2 ] -x,-z,-y        0.0000 0.0000 
    23 [C2 ] -z,-y,-x        0.0031 0.0069  24 [C2 ] -y,-x,-z        0.0031 0.0069 
    25 [C4 ] -z,y,x          0.0084 0.0129  26 [C2 ] y,x,-z          0.0073 0.0106 
    27 [C4 ] x,-z,y          0.0105 0.0144  28 [S6 ] -y,z,x          0.0070 0.0121 
    29 [S6 ] z,x,-y          0.0098 0.0125  30 [Cs ] x,-y,z          0.0063 0.0086 
    31 [S6 ] y,z,-x          0.0070 0.0121  32 [S6 ] z,-x,y          0.0070 0.0121 
    33 [Cs ] -x,y,z          0.0084 0.0130  34 [C4 ] y,-x,z          0.0084 0.0129 
    35 [C2 ] -x,z,y          0.0084 0.0130  36 [C4 ] z,y,-x          0.0084 0.0129 
    37 [Cs ] x,-z,-y         0.0084 0.0130  38 [S4 ] -z,-y,x         0.0084 0.0129 
    39 [S4 ] -y,x,-z         0.0084 0.0129  40 [S4 ] -x,z,-y         0.0105 0.0144 
    41 [S4 ] z,-y,-x         0.0084 0.0129  42 [Cs ] -y,-x,z         0.0073 0.0106 
    43 [Cs ] z,y,x           0.0031 0.0069  44 [Cs ] y,x,z           0.0031 0.0069 
    45 [Cs ] x,z,y           0.0000 0.0000  46 [S4 ] y,-x,-z         0.0084 0.0129 
    47 [S4 ] -x,-z,y         0.0105 0.0144  48 [Cs ] -z,y,-x         0.0073 0.0106 
   

   ---

2. Inter-molecular

   This (experimental) routine attempts to identify symmetry relations between crystallographically independent molecules.

   In general there will be three outcomes of a NONSYM analysis:

   1. A symmetry direction is found compatible with the translation lattice. In such a case, ADDSYM should have indicated what the read space group will be.

   2. A symmetry direction is found that is not compatible with the translation lattice, i.e with a non-zero angle with all translation vectors in the lattice, and thus only local.
      A possible consequence could be disorder/twinning.

   3. No satisfactory local or global (pseudo) symmetry direction.

Instructions

CALC NONSYM

SYMMETRY TOOLS

PLATON HOMEPAGE