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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 === PAP . Provide better documentation for rotating/shifting an image 
Requests
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
PRB
 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 KLH100classaveragesrefined sidewinder model as the reference model
 b 3D reconstruction in /mnt/shared/prbTestKLH/TEST_2/REFI15 KLH single particle 3D reconstruction, which uses KLH100classaveragesrefined randomlyassignedangles model as the reference model
Conclusions
. 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.