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:

    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

The NONSYM feature is invoked either with a left-button-click on NONSYM or from the keyboard:

CALC NONSYM


SYMMETRY TOOLS PLATON HOMEPAGE
26-Sep-2001 A.L.Spek