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   PAP, PRB - how to get angles for a given symmetry group (sample3D)
                      how to get boundaries of an asymmetric unit.
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 . PAP, PRB - how to get angles for a given symmetry group (sample3D)
  . how to get boundaries of an asymmetric unit.
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PRB regarding Sidewinder
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PRB regarding Sidewinder
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.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)
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)
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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)