Feature #2427
closed
eman make3d failure report
Added by Anchi Cheng over 11 years ago.
Updated over 10 years ago.
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.
- 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.
- Status changed from In Code Review to Closed
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