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Comment:

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Deletions are marked like this.  Additions are marked like this. 
Line 18:  Line 18: 
. icos_poss = get_sym_pass( top_face = get_face("icos",3,"mrc")  . icos_poss = get_sym_poss("icos") . Top_face = get_face("icos",3,"mrc") 
Line 24:  Line 25: 
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. Conclusions: Sidewinder gives better initial model than random angle assignement. 
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. Conclusions: Sidewinder gives better initial model than random angle assignement.