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 . PAP, PRB - how  to get angles for a given symmetry group (sample3D)
  . how to get boundaries of an asymmetric unit.
 . PAP, PRB - how to get angles for a given symmetry group (sample3D)
 . how to get the symmetries in the transform class
. how to get boundaries of an asymmetric unit.
  
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Other: threshhold amplitudes

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. (fixed December 10th 2006)

  • PAP, PRB - how to get angles for a given symmetry group (sample3D)
  • how to get the symmetries in the transform class
  • how to get boundaries of an asymmetric unit.

PRB from Transform class paper

  • sample3D(6,asymmetric_unit",theta_range,phi_range,"method");
  • set_rotation(Initial Array, Final Array) ; see paper
  • RA.get_sym("c3",2); # This is a rotation element of 120 degrees
  • icos_poss = get_sym_poss("icos"); # List the possible conventions of the icosahedron
  • Top_face = get_face("icos",3,"mrc"); # represents the vertices of one of faces of the icosahedron
  • RA.get_sym("icos",3,"mrc"); # This allows one to access elements of the icosahedron in the mrc convention
  • RA.get_sym("icos",3, vertex, face); #This gets the third symmetry elements when the vertex and a face are in specified position
  • em_image.py
  • Consolidate some of the rotation calls; Get rid of EMAN calls

PRB regarding Sidewinder

Other: threshhold amplitudes

  • ratcheting move not working 100% correctly

tests on model created by sidewinder:

. 1. KLH

  • a 3D reconstruction 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 3D reconstruction 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 model created in 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 unless we do same correction. (it is difficult, because this requires ctf parameters of particles )

. iv Sidewinder gives better initial model than random angle assignement.

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