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Deletions are marked like this.  Additions are marked like this. 
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1. KLH  . 1. '''KLH''' 
Requests
11/30/06 PAP
Zhong  work on CTF and on highres refinement
12/15/06 PRB
PAP  compose_transform returns negative Eulerian angles sometimes; should always return positive.
 PAP, PRB  how to get angles for a given symmetry group (sample3D)
 how to get boundaries of an asymmetric unit.
PRB from Transform class paper
 sample3D();
 set_rotation(Initial Array, Final Array) ; see paper
 RA.get_sym("c3,2);
 RA.get_sym("icos",3,"orientation")
 RA.get_sym("icos",3, vertex, face);
 RA.get_sym("icos",3, "mrc");
 icos_poss = get_sym_poss("icos")
 Top_face = get_face("icos",3,"mrc")
 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 Results in /mnt/shared/prbTestKLH/TEST_1/REFI15 KLH single particle 3D reconstruction, which uses KLH100classaveragesrefined sidewinder model as the reference model
 b Results 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 a along with the porgress 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
. iv Sidewinder gives better initial model than random angle assignement.