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 . a. Results 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. Results 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
 . a Results 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 Results 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
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. 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. . 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 high-res 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 KLH-100-class-averages-refined sidewinder model as the reference model
  • b Results 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

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