Filament refinement error

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Doulin Shepherd

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Jun 6, 2022, 4:30:59 AM6/6/22
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Hello Eman Team,


I am getting an unexpected error when I try to use the "--curve" command to get an initial model of a filament.

EMAN 2.99 ( GITHUB: 2022-02-16 14:39 - commit: 49f9da41b )

Your EMAN2 is running on: Linux-5.13.0-44-generic-x86_64-with-glibc2.31 5.13.0-44-generic

Your Python version is: 3.9.10


Quick workflow summary:

1. Pick points on the filament using the draw curve tool

2. Press "Interpolate"

3. Close window and open up the particle extraction window

4. Extract the particles from curve "00" with an overlap of 0.5

5. Watch the read out in terminal that indicates that it is ineed extracting from the curves

6. Build set 

7. Run the command below which gives me the error.

Command: 

e2spt_sgd_new.py sets/flag14.lst  --niter 30  --curve


Error:

Gathering metadata...
 151/151
iter 0, class 0:
17 jobs on 12 CPUs
Error executing:  <e2spt_align_subtlt.SptAlignTask object at 0x7f4f1220fd30>
Traceback (most recent call last):
  File "/home/doulin/miniconda3/envs/eman2/bin/e2parallel.py", line 87, in main
    ret=task.execute(empty_func)
  File "/home/doulin/miniconda3/envs/eman2/bin/e2spt_align_subtlt.py", line 474, in execute
    score=newscore[0]
UnboundLocalError: local variable 'newscore' referenced before assignment

Error executing:  <e2spt_align_subtlt.SptAlignTask object at 0x7f95c9a0ed30>
Traceback (most recent call last):
  File "/home/doulin/miniconda3/envs/eman2/bin/e2parallel.py", line 87, in main
    ret=task.execute(empty_func)
  File "/home/doulin/miniconda3/envs/eman2/bin/e2spt_align_subtlt.py", line 474, in execute
    score=newscore[0]
UnboundLocalError: local variable 'newscore' referenced before assignment

Error executing:  <e2spt_align_subtlt.SptAlignTask object at 0x7fe77ca04d30>
Traceback (most recent call last):
  File "/home/doulin/miniconda3/envs/eman2/bin/e2parallel.py", line 87, in main
    ret=task.execute(empty_func)
  File "/home/doulin/miniconda3/envs/eman2/bin/e2spt_align_subtlt.py", line 474, in execute
    score=newscore[0]
UnboundLocalError: local variable 'newscore' referenced before assignment

Error executing:  <e2spt_align_subtlt.SptAlignTask object at 0x7fe888117d30>
Error executing:  <e2spt_align_subtlt.SptAlignTask object at 0x7fcbe4b11d30>
Traceback (most recent call last):
  File "/home/doulin/miniconda3/envs/eman2/bin/e2parallel.py", line 87, in main
    ret=task.execute(empty_func)
  File "/home/doulin/miniconda3/envs/eman2/bin/e2spt_align_subtlt.py", line 474, in execute
    score=newscore[0]
UnboundLocalError: local variable 'newscore' referenced before assignment

Traceback (most recent call last):
  File "/home/doulin/miniconda3/envs/eman2/bin/e2parallel.py", line 87, in main
    ret=task.execute(empty_func)
  File "/home/doulin/miniconda3/envs/eman2/bin/e2spt_align_subtlt.py", line 474, in execute
    score=newscore[0]
UnboundLocalError: local variable 'newscore' referenced before assignment

Error executing:  <e2spt_align_subtlt.SptAlignTask object at 0x7f8f5d89fd30>
Traceback (most recent call last):
  File "/home/doulin/miniconda3/envs/eman2/bin/e2parallel.py", line 87, in main
    ret=task.execute(empty_func)
  File "/home/doulin/miniconda3/envs/eman2/bin/e2spt_align_subtlt.py", line 474, in execute
    score=newscore[0]
UnboundLocalError: local variable 'newscore' referenced before assignment

Error executing:  <e2spt_align_subtlt.SptAlignTask object at 0x7f3aa4c11d30>
Error executing:  <e2spt_align_subtlt.SptAlignTask object at 0x7f90b8f61d30>
Traceback (most recent call last):
  File "/home/doulin/miniconda3/envs/eman2/bin/e2parallel.py", line 87, in main
    ret=task.execute(empty_func)
  File "/home/doulin/miniconda3/envs/eman2/bin/e2spt_align_subtlt.py", line 474, in execute
    score=newscore[0]
UnboundLocalError: local variable 'newscore' referenced before assignment

Traceback (most recent call last):
  File "/home/doulin/miniconda3/envs/eman2/bin/e2parallel.py", line 87, in main
    ret=task.execute(empty_func)
  File "/home/doulin/miniconda3/envs/eman2/bin/e2spt_align_subtlt.py", line 474, in execute
    score=newscore[0]
UnboundLocalError: local variable 'newscore' referenced before assignment

Error executing:  <e2spt_align_subtlt.SptAlignTask object at 0x7ffb37131d30>
Traceback (most recent call last):
  File "/home/doulin/miniconda3/envs/eman2/bin/e2parallel.py", line 87, in main
    ret=task.execute(empty_func)
  File "/home/doulin/miniconda3/envs/eman2/bin/e2spt_align_subtlt.py", line 474, in execute
    score=newscore[0]
UnboundLocalError: local variable 'newscore' referenced before assignment

Error executing:  <e2spt_align_subtlt.SptAlignTask object at 0x7f1b5e55dd30>
Traceback (most recent call last):
  File "/home/doulin/miniconda3/envs/eman2/bin/e2parallel.py", line 87, in main
    ret=task.execute(empty_func)
  File "/home/doulin/miniconda3/envs/eman2/bin/e2spt_align_subtlt.py", line 474, in execute
    score=newscore[0]
UnboundLocalError: local variable 'newscore' referenced before assignment

Error executing:  <e2spt_align_subtlt.SptAlignTask object at 0x7f57f46acd30>
Traceback (most recent call last):
  File "/home/doulin/miniconda3/envs/eman2/bin/e2parallel.py", line 87, in main
    ret=task.execute(empty_func)
  File "/home/doulin/miniconda3/envs/eman2/bin/e2spt_align_subtlt.py", line 474, in execute
    score=newscore[0]
UnboundLocalError: local variable 'newscore' referenced before assignment

Error executing:  <e2spt_align_subtlt.SptAlignTask object at 0x7f18d179fd30>
Traceback (most recent call last):
  File "/home/doulin/miniconda3/envs/eman2/bin/e2parallel.py", line 87, in main
    ret=task.execute(empty_func)
  File "/home/doulin/miniconda3/envs/eman2/bin/e2spt_align_subtlt.py", line 474, in execute
    score=newscore[0]
UnboundLocalError: local variable 'newscore' referenced before assignment

Error running task :  0
Traceback (most recent call last):
  File "/home/doulin/miniconda3/envs/eman2/bin/e2spt_sgd_new.py", line 236, in <module>
    main()
  File "/home/doulin/miniconda3/envs/eman2/bin/e2spt_sgd_new.py", line 138, in main
    a3dout.append(load_lst_params(f"{path}/aliptcls3d_00.lst"))
  File "/home/doulin/miniconda3/envs/eman2/lib/python3.9/site-packages/EMAN2.py", line 2841, in load_lst_params
    lsx=LSXFile(fsp,True)
  File "/home/doulin/miniconda3/envs/eman2/lib/python3.9/site-packages/EMAN2.py", line 2477, in __init__
    if ifexists: raise Exception("Error: lst file {} does not exist".format(path))
Exception: Error: lst file sptsgd_01/aliptcls3d_00.lst does not exist
Exception ignored in: <function LSXFile.__del__ at 0x7fda46b0e430>
Traceback (most recent call last):
  File "/home/doulin/miniconda3/envs/eman2/lib/python3.9/site-packages/EMAN2.py", line 2543, in __del__
    self.close()
  File "/home/doulin/miniconda3/envs/eman2/lib/python3.9/site-packages/EMAN2.py", line 2554, in close
    if self.ptr!=None :
AttributeError: 'LSXFile' object has no attribute 'ptr'


Cheers,

Doulin Shepherd

PhD student

Department of Biochemistry & Pharmacology,

Bio21 Molecular Science and Biotechnology Institute

The University of Melbourne, Victoria, 3010 Australia

MuyuanChen

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Jun 6, 2022, 1:07:38 PM6/6/22
to em...@googlegroups.com
What is the particle box size and apix? Do you trigger the same error if you change —res to 30 or lower in the e2spt_sgd_new command?

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Doulin Shepherd

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Jun 6, 2022, 8:11:40 PM6/6/22
to EMAN2
The a/pix is 8.240 in the binned 1K tomogram and my unbinned box size is 64 (I started with a binned 2K tilt series) 

Changing it to --res 15 worked,  I usually leave the --res default does filament mode require a specific res target?

Cheers,
Doulin

Muyuan Chen

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Jun 6, 2022, 9:51:45 PM6/6/22
to em...@googlegroups.com
I think it is because at the given box size and apix, there isn’t enough Fourier voxels to do the first round of alignment, since the default —res is 50. Unless you have very good signal, I don’t think —res=15 is a great idea though. Maybe using a bigger box size and —res=30 or higher.

On Jun 6, 2022, at 5:11 PM, Doulin Shepherd <doulin....@gmail.com> wrote:

The a/pix is 8.240 in the binned 1K tomogram and my unbinned box size is 64 (I started with a binned 2K tilt series) 
Message has been deleted

Doulin Shepherd

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Jun 7, 2022, 2:14:54 AM6/7/22
to EMAN2
That fixed it thank you!
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