Differences between revisions 12 and 13
Revision 12 as of 2006-12-18 19:23:30
Size: 1798
Editor: bmb14
Comment:
Revision 13 as of 2006-12-18 19:24:57
Size: 1803
Editor: bmb14
Comment:
Deletions are marked like this. Additions are marked like this.
Line 26: Line 26:
1. KLH:
a. Results in /mnt/shared/prbTestKLH/TEST_1/REFI15
.1. KLH:
.a. Results in /mnt/shared/prbTestKLH/TEST_1/REFI15
Line 29: Line 29:
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.
.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.
Line 33: Line 33:
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
.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
Line 36: Line 36:
Conclusions: .Conclusions:.
Line 38: Line 38:

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)