Icosahedral Reconstructions

in SPIDER

• The reference structure has to be placed such that the 5-fold symmetry axis is on Z-axis.
• Any refinement program (from Three Dimensional Reconstruction of Single Particle Specimens using Reference Projections) can be used with the following modifications:
• Alignment operations should not check mirrored positions (see AP SH)
• VO EA operation that appears in these procedures has to be modified such that the unique triangle specified is:
  theta = 0,37
  phi = 0,71.999
  
• The 3D reconstruction operations need a icosahedral symmetry document file which is given below. Here is the same file for downloading: ico_symm.txt

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  Iscosahedral Symmetries Document File

    ;   Angles  psi, theta, phi
       1 3      0.0000      0.0000      0.0000
       2 3      0.0000      0.0000     72.0000
       3 3      0.0000      0.0000    144.0000
       4 3      0.0000      0.0000    216.0000
       5 3      0.0000      0.0000    288.0000
       6 3      0.0000     63.4349     36.0000
       7 3      0.0000     63.4349    108.0000
       8 3      0.0000     63.4349    180.0000
       9 3      0.0000     63.4349    252.0000
      10 3      0.0000     63.4349    324.0000
      11 3     72.0000     63.4349     36.0000
      12 3     72.0000     63.4349    108.0000
      13 3     72.0000     63.4349    180.0000
      14 3     72.0000     63.4349    252.0000
      15 3     72.0000     63.4349    324.0000
      16 3    144.0000     63.4349     36.0000
      17 3    144.0000     63.4349    108.0000
      18 3    144.0000     63.4349    180.0000
      19 3    144.0000     63.4349    252.0000
      20 3    144.0000     63.4349    324.0000
      21 3    216.0000     63.4349     36.0000
      22 3    216.0000     63.4349    108.0000
      23 3    216.0000     63.4349    180.0000
      24 3    216.0000     63.4349    252.0000
      25 3    216.0000     63.4349    324.0000
      26 3    288.0000     63.4349     36.0000
      27 3    288.0000     63.4349    108.0000
      28 3    288.0000     63.4349    180.0000
      29 3    288.0000     63.4349    252.0000
      30 3    288.0000     63.4349    324.0000
      31 3     36.0000    116.5651      0.0000
      32 3     36.0000    116.5651     72.0000
      33 3     36.0000    116.5651    144.0000
      34 3     36.0000    116.5651    216.0000
      35 3     36.0000    116.5651    288.0000
      36 3    108.0000    116.5651      0.0000
      37 3    108.0000    116.5651     72.0000
      38 3    108.0000    116.5651    144.0000
      39 3    108.0000    116.5651    216.0000
      40 3    108.0000    116.5651    288.0000
      41 3    180.0000    116.5651      0.0000
      42 3    180.0000    116.5651     72.0000
      43 3    180.0000    116.5651    144.0000
      44 3    180.0000    116.5651    216.0000
      45 3    180.0000    116.5651    288.0000
      46 3    252.0000    116.5651      0.0000
      47 3    252.0000    116.5651     72.0000
      48 3    252.0000    116.5651    144.0000
      49 3    252.0000    116.5651    216.0000
      50 3    252.0000    116.5651    288.0000
      51 3    324.0000    116.5651      0.0000
      52 3    324.0000    116.5651     72.0000
      53 3    324.0000    116.5651    144.0000
      54 3    324.0000    116.5651    216.0000
      55 3    324.0000    116.5651    288.0000
      56 3      0.0000    180.0000      0.0000
      57 3      0.0000    180.0000     72.0000
      58 3      0.0000    180.0000    144.0000
      59 3      0.0000    180.0000    216.0000
      60 3      0.0000    180.0000    288.0000
  

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  See also the Principles behind the icosahedral reconstruction programs published in J. Struct Biol 116:48-55 (1996).