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Feature #2427

closed

eman make3d failure report

Added by Anchi Cheng over 11 years ago. Updated over 10 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Amber Herold
Category:
-
Target version:
Appion/Leginon 3.0.0
Start date:
07/18/2013
Due date:
% Done:

0%

Estimated time:

Description

eman refine includes the running of make3d which may fail even though classes are formed since projection matching allows a projection to fall into some class even if the phase error is high. There is some rejection criteria in make3d (a subprogram run by refine). When the mask is too tight or "hard" is to small (appears to be a phase error threshold, though not well documented), all images would be rejected and therefore gives an empty volume.

This should be reported in the job log and suggestion made to the user.

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 #1

Updated by Anchi Cheng over 11 years ago

  • Status changed from Assigned to In Code Review
  • Assignee changed from Anchi Cheng to Amber Herold

r17758 added this.

Another sign of trouble:

refine*.txt shows something like this when all images are rejected

Run 'make3d help' for detailed help.
Read data
Transform slices
0/20(1)  1    0.0  232.0    0.0 5.130952  58.599383  X
1/20(3)  2    4.0  234.0  356.5 5.413873  56.488663  X
2/20(5)  3    4.0  251.1  359.5 6.260561  44.759343  X
3/20(11)  1  12.0  234.0    2.5 5.481109  56.285659  X
4/20(13)  1  12.0  251.1    1.5 5.292427  49.975186  X
5/20(15)  3  16.0  234.0    0.5 5.748035  41.336687  X
6/20(17)  4  16.0  251.1    0.5 6.240679  32.747482  X
7/20(19)  4  20.0  234.0  359.5 6.199037  45.161914  X
8/20(21)  5  20.0  251.1    0.0 6.308959  28.197464  X
9/20(23)  1  24.0  234.0    0.0 5.606518  55.014578  X
10/20(25)  8   24.0  246.0  359.5 6.075042  25.675668  X
11/20(27)  5   24.0  258.0    0.5 6.489682  23.210796  X
12/20(29)  2   28.0  234.0  359.5 5.782136  54.759918  X
13/20(31)  7   28.0  244.3    0.0 6.170562  22.250098  X
14/20(33)  10  28.0  254.6  359.5 6.106928  23.315829  X
15/20(35)  3   28.0  264.9    0.0 5.575979  41.541614  X
16/20(37)  1   32.0  243.0    3.5 5.533533  58.757153  X
17/20(39)  7   32.0  252.0    0.0 6.232655  24.952382  X
18/20(41)  6   32.0  261.0    0.0 6.472377  22.259458  X
19/20(43)  3   36.0  266.0    0.0 5.947117  36.253182  X
Phase error Mean=40.077122   Sigma=13.525136   used 0/77 images

Testing: start 1 iteration of EMAN refinement on a small image stack and gives the mask raidus so small that it clips into the density of the protein. For example, input mask radius of 200 A for the 350 A rotavirus.

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 #2

Updated by Amber Herold over 10 years ago

  • Status changed from In Code Review to Closed
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