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  . 3/26/07 Phil, can you please document how to relate chimer params to SPARX params? PAP.

  . 2/6/07 now exists runSidewinder; which is in the documentation, but not committed yet: need to make sure Sidewinder is not importing too much.

 .the priority remains scale in linear interpolation... 2/12/2007
  .see /home/prb/sparx/test/3DA/test_rot.py
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=== done some 01/03/07 needs more work ===
 . Provide better documentation for rotating/shifting an image


PRB from Transform class paper

  • sample3D(6,asymmetric_unit",theta_range,phi_range,"method");

need to include different versions of the icosahedron

  • Fix symmetry in wbp
  • set_rotation(Initial Array, Final Array) ; see paper
  • RA.get_sym("c3",2); # This is a rotation element of 120 degrees
  • icos_poss = get_sym_poss("icos"); # List the possible conventions of the icosahedron
  • Top_face = get_face("icos",3,"mrc"); # represents the vertices of one of faces of the icosahedron
  • RA.get_sym("icos",3,"mrc"); # This allows one to access elements of the icosahedron in the mrc convention
  • RA.get_sym("icos",3, vertex, face); #This gets the third symmetry elements when the vertex and a face are in specified position
  • em_image.py
  • Consolidate some of the rotation calls; Get rid of EMAN calls

PRB regarding Sidewinder

  • ratcheting move not working 100% correctly


  • tests on model created by sidewinder:

. 1. KLH

  • a 3D reconstruction in /mnt/shared/prbTestKLH/TEST_1/REFI15 KLH single particle 3D reconstruction, which uses KLH-100-class-averages-refined sidewinder model as the reference model
  • b 3D reconstruction in /mnt/shared/prbTestKLH/TEST_2/REFI15 KLH single particle 3D reconstruction, which uses KLH-100-class-averages-refined randomly-assigned-angles model as the reference model


. i 3D volumes in a has better resolutions (FRC) than 3D volumes in b in the initial iterations of 3D reconstructions. a is also more similiar to the published model than b. (high cross correlation value)

. ii b converges to model created in a along with the progress of 3D refinement

. iii The published model could be applied CTF corrections. Hence, we cannot use FRC to compare the similarity between currently reconstructed two models with the published model unless we do same correction. (it is difficult, because this requires ctf parameters of particles )

. iv Sidewinder gives better initial model than random angle assignement.

Requests (last edited 2017-05-07 11:49:13 by penczek)