Error for EMAN2 sub-tilt refine.

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Si Hoon Park

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Jan 9, 2022, 11:56:30 PM1/9/22

to EMAN2

Dear EMAN2,

I got an error during sub-tilt refinement.

Previously, there was no such error. so I did not understand what is problem.. can I get some help?

Sincerely,

Si Hoon Park

----------------------------------------------------

Start from a spt refinement...
Writing to spt_13_07...
loading 1600 3D particles from a192ctf
box size 192, apix 2.30
Apix mismatch between 2D and 3D particles: 2.30 vs 2.30
Will scale translation by 1.0 ...
Keeping 1280 good 3D particles with ptclkeep ...
Building aligned 2D particle set from spt alignment...
e2spt_tiltrefine_oneiter.py --ptclin spt_13_07/ali_ptcls_00_even.lst --ptclout spt_13_07/ali_ptcls_01_even.lst --ref spt_13_07/threed_00_even.hdf --threedout spt_13_07/threed_01_even.hdf --keep 0.8 --threads 24 --parallel thread:24 --refineastep 1.0 --refinentry 8 --maxshift 8 --padby 1.5 --sym c1
Initializing parallelism...
24 total CPUs available
19170 jobs
Error running task : 2
e2proc3d.py spt_13_07/threed_01_even.hdf spt_13_07/threed_raw_even.hdf
Traceback (most recent call last):
File "/home/eman/eman2-sphire-sparx/lib/python3.7/site-packages/EMAN2db.py", line 657, in db_get_image_count
ret = EMUtil.get_image_count_c(fsp)
RuntimeError: FileAccessException at /home/eman2/miniconda3/conda-bld/eman2_1615224802990/work/libEM/io/hdfio2.cpp:464: error with 'spt_13_07/threed_01_even.hdf': 'cannot access file 'spt_13_07/threed_01_even.hdf'' caught

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/eman/eman2-sphire-sparx/bin/e2proc3d.py", line 890, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2proc3d.py", line 308, in main
else : nimg = EMUtil.get_image_count(infile)
File "/home/eman/eman2-sphire-sparx/lib/python3.7/site-packages/EMAN2db.py", line 660, in db_get_image_count
raise Exception(fsp)
Exception: spt_13_07/threed_01_even.hdf
e2spt_tiltrefine_oneiter.py --ptclin spt_13_07/ali_ptcls_00_odd.lst --ptclout spt_13_07/ali_ptcls_01_odd.lst --ref spt_13_07/threed_00_odd.hdf --threedout spt_13_07/threed_01_odd.hdf --keep 0.8 --threads 24 --parallel thread:24 --refineastep 1.0 --refinentry 8 --maxshift 8 --padby 1.5 --sym c1
Initializing parallelism...
24 total CPUs available
19260 jobs
Error running task : 12
e2proc3d.py spt_13_07/threed_01_odd.hdf spt_13_07/threed_raw_odd.hdf
Traceback (most recent call last):
File "/home/eman/eman2-sphire-sparx/lib/python3.7/site-packages/EMAN2db.py", line 657, in db_get_image_count
ret = EMUtil.get_image_count_c(fsp)
RuntimeError: FileAccessException at /home/eman2/miniconda3/conda-bld/eman2_1615224802990/work/libEM/io/hdfio2.cpp:464: error with 'spt_13_07/threed_01_odd.hdf': 'cannot access file 'spt_13_07/threed_01_odd.hdf'' caught

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/eman/eman2-sphire-sparx/bin/e2proc3d.py", line 890, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2proc3d.py", line 308, in main
else : nimg = EMUtil.get_image_count(infile)
File "/home/eman/eman2-sphire-sparx/lib/python3.7/site-packages/EMAN2db.py", line 660, in db_get_image_count
raise Exception(fsp)
Exception: spt_13_07/threed_01_odd.hdf
e2refine_postprocess.py --even spt_13_07/threed_01_even.hdf --odd spt_13_07/threed_01_odd.hdf --output spt_13_07/threed_01.hdf --iter 1 --restarget 16.984618729278765 --threads 24 --sym c1 --mass 3000.0 --setsf None --tophat localwiener
Mon Jan 10 13:41:01 2022: e2proc3d.py spt_13_07/threed_01_even.hdf spt_13_07/fsc_unmasked_01.txt --calcfsc=spt_13_07/threed_01_odd.hdf
Traceback (most recent call last):
File "/home/eman/eman2-sphire-sparx/lib/python3.7/site-packages/EMAN2db.py", line 657, in db_get_image_count
ret = EMUtil.get_image_count_c(fsp)
RuntimeError: FileAccessException at /home/eman2/miniconda3/conda-bld/eman2_1615224802990/work/libEM/io/hdfio2.cpp:464: error with 'spt_13_07/threed_01_even.hdf': 'cannot access file 'spt_13_07/threed_01_even.hdf'' caught

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/eman/eman2-sphire-sparx/bin/e2proc3d.py", line 890, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2proc3d.py", line 308, in main
else : nimg = EMUtil.get_image_count(infile)
File "/home/eman/eman2-sphire-sparx/lib/python3.7/site-packages/EMAN2db.py", line 660, in db_get_image_count
raise Exception(fsp)
Exception: spt_13_07/threed_01_even.hdf
Error running: e2proc3d.py spt_13_07/threed_01_even.hdf spt_13_07/fsc_unmasked_01.txt --calcfsc=spt_13_07/threed_01_odd.hdf
Traceback (most recent call last):
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine.py", line 539, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine.py", line 460, in main
fsc=np.loadtxt(os.path.join(path, "fsc_masked_{:02d}.txt".format(itr+1)))
File "/home/eman/eman2-sphire-sparx/lib/python3.7/site-packages/numpy/lib/npyio.py", line 968, in loadtxt
fh = np.lib._datasource.open(fname, 'rt', encoding=encoding)
File "/home/eman/eman2-sphire-sparx/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 269, in open
return ds.open(path, mode, encoding=encoding, newline=newline)
File "/home/eman/eman2-sphire-sparx/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 623, in open
raise IOError("%s not found." % path)
OSError: spt_13_07/fsc_masked_01.txt not found.

Si Hoon Park

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Jan 10, 2022, 8:42:40 PM1/10/22

to EMAN2

Dear EMAN2,

It was fixed by just rebooting my workstation.. Now it is working very well.

Best regards

Si Hoon

2022년 1월 10일 월요일 오후 1시 56분 30초 UTC+9에 Si Hoon Park님이 작성:

Si Hoon Park

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Jan 11, 2022, 9:15:53 AM1/11/22

to EMAN2

Dear EMAN2,

I thought it was fixed, however the error was remained..

Strangely, other data set in another project folder was no problem, and 3D refinement/sub-tilt refine were well worked..

Could you help me ?

Best regards

Si Hoon

2022년 1월 11일 화요일 오전 10시 42분 40초 UTC+9에 Si Hoon Park님이 작성:

Ludtke, Steven J.

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Jan 11, 2022, 9:24:24 AM1/11/22

to em...@googlegroups.com

If you see an error like:

Error running task : 2

check the thread.out file, which will contain error messages from individual threads. The output on the screen doesn't give enough information to tell what specifically failed.

You can also try running

e2iminfo.py --check spt_13_07/ali_ptcls_00_even.lst

(the input file).

This will check to make sure that there aren't any 'missing' images in the input.

--------------------------------------------------------------------------------------

Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 
Charles C. Bell Jr., Professor of Structural Biology

Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu)

Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)

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박시훈

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Jan 11, 2022, 10:07:46 AM1/11/22

to em...@googlegroups.com

Dear Steve,

I tried e2iminfo.py, the result showed like this;

------------------------

(base) [eman@lsb01 1xb_eman]$ e2iminfo.py --check spt_13_03/ali_ptcls_00_even.lst spt_13/threed_10.hdf
spt_13_03/ali_ptcls_00_even.lst 19050 images in Fast LST format 384 x 384
spt_13/threed_10.hdf 1 images in HDF5 format (swap) 192 x 192 x 192
Error with CTF on spt_13/threed_10.hdf 0
19051 total images
representing 0 particles

------------------------

and I also attached thread.out file which was complicated more..

------------------------------

Traceback (most recent call last):

File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2spt_align.py", line 537, in execute
b=EMData(fsp,i)
File "/home/eman/eman2-sphire-sparx/lib/python3.7/site-packages/EMAN2db.py", line 400, in db_emd_init
self.__initc(*parms)
RuntimeError: ImageReadException at /home/eman2/miniconda3/conda-bld/eman2_1615224802990/work/libEM/io/hdfio2.cpp:624: error with 'particles3d/SG42bx1_ali__a192ctf.hdf': 'Image 118 does not exist' caught

File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine_oneiter.py", line 292, in execute
c=img.xform_align_nbest("rotate_translate_2d_to_3d_tree",ref, alignpm, 1)
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine_oneiter.py", line 292, in execute
c=img.xform_align_nbest("rotate_translate_2d_to_3d_tree",ref, alignpm, 1)
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine_oneiter.py", line 292, in execute
c=img.xform_align_nbest("rotate_translate_2d_to_3d_tree",ref, alignpm, 1)
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine_oneiter.py", line 292, in execute
c=img.xform_align_nbest("rotate_translate_2d_to_3d_tree",ref, alignpm, 1)
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine_oneiter.py", line 292, in execute
c=img.xform_align_nbest("rotate_translate_2d_to_3d_tree",ref, alignpm, 1)
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine_oneiter.py", line 292, in execute
c=img.xform_align_nbest("rotate_translate_2d_to_3d_tree",ref, alignpm, 1)
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine_oneiter.py", line 292, in execute
c=img.xform_align_nbest("rotate_translate_2d_to_3d_tree",ref, alignpm, 1)
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine_oneiter.py", line 292, in execute
c=img.xform_align_nbest("rotate_translate_2d_to_3d_tree",ref, alignpm, 1)
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine_oneiter.py", line 292, in execute
c=img.xform_align_nbest("rotate_translate_2d_to_3d_tree",ref, alignpm, 1)
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine_oneiter.py", line 292, in execute
c=img.xform_align_nbest("rotate_translate_2d_to_3d_tree",ref, alignpm, 1)
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine_oneiter.py", line 292, in execute
c=img.xform_align_nbest("rotate_translate_2d_to_3d_tree",ref, alignpm, 1)
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine_oneiter.py", line 292, in execute
c=img.xform_align_nbest("rotate_translate_2d_to_3d_tree",ref, alignpm, 1)
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine_oneiter.py", line 292, in execute
c=img.xform_align_nbest("rotate_translate_2d_to_3d_tree",ref, alignpm, 1)
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine_oneiter.py", line 292, in execute
c=img.xform_align_nbest("rotate_translate_2d_to_3d_tree",ref, alignpm, 1)
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine_oneiter.py", line 292, in execute
c=img.xform_align_nbest("rotate_translate_2d_to_3d_tree",ref, alignpm, 1)
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine_oneiter.py", line 292, in execute
c=img.xform_align_nbest("rotate_translate_2d_to_3d_tree",ref, alignpm, 1)
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine_oneiter.py", line 292, in execute
c=img.xform_align_nbest("rotate_translate_2d_to_3d_tree",ref, alignpm, 1)
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine_oneiter.py", line 222, in execute
img=EMData(info[1],info[0])
File "/home/eman/eman2-sphire-sparx/lib/python3.7/site-packages/EMAN2db.py", line 400, in db_emd_init
self.__initc(*parms)
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine_oneiter.py", line 222, in execute
img=EMData(info[1],info[0])
File "/home/eman/eman2-sphire-sparx/lib/python3.7/site-packages/EMAN2db.py", line 400, in db_emd_init
self.__initc(*parms)
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine_oneiter.py", line 292, in execute
c=img.xform_align_nbest("rotate_translate_2d_to_3d_tree",ref, alignpm, 1)
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine_oneiter.py", line 292, in execute
c=img.xform_align_nbest("rotate_translate_2d_to_3d_tree",ref, alignpm, 1)
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine_oneiter.py", line 292, in execute
c=img.xform_align_nbest("rotate_translate_2d_to_3d_tree",ref, alignpm, 1)
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine_oneiter.py", line 292, in execute
c=img.xform_align_nbest("rotate_translate_2d_to_3d_tree",ref, alignpm, 1)
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine_oneiter.py", line 292, in execute
c=img.xform_align_nbest("rotate_translate_2d_to_3d_tree",ref, alignpm, 1)
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine_oneiter.py", line 292, in execute
c=img.xform_align_nbest("rotate_translate_2d_to_3d_tree",ref, alignpm, 1)
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine_oneiter.py", line 292, in execute
c=img.xform_align_nbest("rotate_translate_2d_to_3d_tree",ref, alignpm, 1)
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine_oneiter.py", line 292, in execute
c=img.xform_align_nbest("rotate_translate_2d_to_3d_tree",ref, alignpm, 1)
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine_oneiter.py", line 292, in execute
c=img.xform_align_nbest("rotate_translate_2d_to_3d_tree",ref, alignpm, 1)
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine_oneiter.py", line 292, in execute
c=img.xform_align_nbest("rotate_translate_2d_to_3d_tree",ref, alignpm, 1)
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine_oneiter.py", line 292, in execute
c=img.xform_align_nbest("rotate_translate_2d_to_3d_tree",ref, alignpm, 1)
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine_oneiter.py", line 292, in execute
c=img.xform_align_nbest("rotate_translate_2d_to_3d_tree",ref, alignpm, 1)
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 102, in <module>
main()
File "/home/eman/eman2-sphire-sparx/bin/e2parallel.py", line 86, in main
try: dump(task.execute(empty_func),open(options.taskout,"wb"),-1)
File "/home/eman/eman2-sphire-sparx/bin/e2spt_tiltrefine_oneiter.py", line 292, in execute
c=img.xform_align_nbest("rotate_translate_2d_to_3d_tree",ref, alignpm, 1)

Traceback (most recent call last):

File "/opt/e2test/bin/e2parallel.py", line 87, in main
ret=task.execute(empty_func)
File "/opt/e2test/bin/e2spt_tiltrefine_oneiter.py", line 280, in execute
d={"type":"eman","tx":initxf["tx"], "ty":initxf["ty"]}
TypeError: 'Transform' object is not subscriptable

Traceback (most recent call last):

---------------------

Sincerely,

Si Hoon

2022년 1월 11일 (화) 오후 11:24, Ludtke, Steven J. <slu...@bcm.edu>님이 작성:

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/980D0240-D996-4E16-BA62-6C84B393386A%40bcm.edu.

Ludtke, Steven J.

unread,

Jan 11, 2022, 10:38:18 AM1/11/22

to em...@googlegroups.com

Well, the immediate issue is pretty obvious from the beginning of the file:

FileAccessException at /home/eman2/miniconda3/conda-bld/eman2_1615224802990/work/libEM/io/lstfastio.cpp:162: error with 'particles3d/NC4bx1_ali__a192ctf.hdf': 'cannot access file 'particles3d/NC4bx1_ali__a192ctf.hdf'' caught

one (or more) of the image files referenced in the .lst file being used as an input is either missing or cannot be accessed due to permissions. Are you running the refinement from the project folder? Try:

e2iminfo --check particles3d/NC4bx1_ali__a192ctf.hdf

Anyway, for some reason it is having issues with one or more of your image files...

박시훈

unread,

Jan 11, 2022, 11:19:25 AM1/11/22

to em...@googlegroups.com

Dear Steve,

Thank you for your kind answer.

I tried e2iminfo.py, and the following script was shown;

lsb02 1xb_eman]$ e2iminfo.py check particles3d/NC4bx1_ali__a192ctf.hdf
check is not a recognized image format
particles3d/NC4bx1_ali__a192ctf.hdf 220 images in HDF5 format (swap) 192 x 192 x 192
220 total images

I refined the model in the project folder (maybe always..) and indeed, several refinements were well done from getting the initial model to subtilt refinement.

Although using a re-extracted particles set, it showed similar error messages with the reference 'spt13'... Now, I have started to generate an initial model using the re-extracted particles set and a previous job 'spt10' as a reference model, and it looks pretty good without error messages so far..

Best regards,

Si Hoon

2022년 1월 12일 (수) 오전 12:38, Ludtke, Steven J. <slu...@bcm.edu>님이 작성:

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Ludtke, Steven J.

unread,

Jan 11, 2022, 11:31:24 AM1/11/22

to em...@googlegroups.com

You missed the -- in front of check

--------------------------------------------------------------------------------------

Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 
Charles C. Bell Jr., Professor of Structural Biology

Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu)

Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/CALP%3Dy6L58JDLhNT86wTS3N-R2-zNaHt3EgxYUOWX7fjtbBhMwA%40mail.gmail.com.

박시훈

unread,

Jan 11, 2022, 5:19:09 PM1/11/22

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Dear Steve,

Is there any missing point in CTF information or related factors?

I checked the wiener filter option during particle extraction.

(base) [eman@lsb02 1xb_eman]$ e2iminfo.py --check particles3d/NC4bx1_ali__a192ctf.hdf

particles3d/NC4bx1_ali__a192ctf.hdf 220 images in HDF5 format (swap) 192 x 192 x 192

Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 0
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 1
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 2
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 3
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 4
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 5
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 6
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 7
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 8
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 9
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 10
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 11
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 12
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 13
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 14
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 15
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 16
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 17
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 18
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 19
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 20
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 21
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 22
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 23
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 24
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 25
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 26
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 27
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 28
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 29
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 30
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 31
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 32
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 33
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 34
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 35
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 36
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 37
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 38
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 39
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 40
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 41
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 42
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 43
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 44
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 45
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 46
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 47
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 48
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 49
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 50
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 51
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 52
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 53
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 54
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 55
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 56
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 57
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 58
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 59
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 60
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 61
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 62
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 63
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 64
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 65
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 66
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 67
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 68
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 69
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 70
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 71
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 72
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 73
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 74
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 75
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 76
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 77
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 78
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 79
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 80
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 81
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 82
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 83
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 84
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 85
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 86
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 87
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 88
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 89
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 90
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 91
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 92
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 93
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 94
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 95
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 96
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 97
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 98
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 99
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 100
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 101
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 102
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 103
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 104
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 105
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 106
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 107
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 108
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 109
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 110
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 111
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 112
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 113
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 114
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 115
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 116
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 117
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 118
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 119
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 120
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 121
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 122
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 123
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 124
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 125
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 126
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 127
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 128
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 129
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 130
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 131
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 132
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 133
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 134
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 135
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 136
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 137
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 138
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 139
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 140
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 141
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 142
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 143
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 144
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 145
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 146
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 147
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 148
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 149
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 150
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 151
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 152
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 153
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 154
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 155
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 156
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 157
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 158
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 159
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 160
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 161
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 162
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 163
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 164
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 165
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 166
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 167
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 168
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 169
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 170
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 171
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 172
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 173
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 174
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 175
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 176
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 177
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 178
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 179
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 180
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 181
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 182
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 183
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 184
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 185
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 186
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 187
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 188
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 189
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 190
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 191
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 192
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 193
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 194
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 195
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 196
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 197
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 198
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 199
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 200
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 201
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 202
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 203
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 204
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 205
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 206
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 207
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 208
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 209
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 210
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 211
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 212
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 213
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 214
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 215
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 216
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 217
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 218
Error with CTF on particles3d/NC4bx1_ali__a192ctf.hdf 219
220 total images
representing 0 particles

Best regards

Si Hoon

2022년 1월 12일 (수) 오전 1:31, Ludtke, Steven J. <slu...@bcm.edu>님이 작성:

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/FC0DB8A1-0E99-4DFE-8B61-6ABB09E8DA65%40bcm.edu.

Ludtke, Steven J.

unread,

Jan 11, 2022, 6:14:19 PM1/11/22

to em...@googlegroups.com

3d particles don't have CTF information, since they are aggregates of many different CTFs. You could try "--all --stat" instead of "--check" in that case. If you see statistics for all of the particles, and no errors, then the file is fine.

Again, though, the real point is:

cannot access file 'particles3d/NC4bx1_ali__a192ctf.hdf'

This really implies that the program was run from the wrong folder (ie - particles3d/ doesn't exist where the program was run) or some odd file permissions issue.

--------------------------------------------------------------------------------------

Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 
Charles C. Bell Jr., Professor of Structural Biology

Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu)

Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/CALP%3Dy6LaFQbYFPR44-Eyb6pcRCPsJBMiqY6p_nVuVB8i9cOVzg%40mail.gmail.com.

박시훈

unread,

Jan 11, 2022, 8:38:20 PM1/11/22

to em...@googlegroups.com

Dear Steve,

Thank you for your reply.

I tried "chmod -R 777" to solve the permission error, but it was not solved.

The "--all --stat" result looks fine.

I re-extracted the same particles with same manner, and got a similar initial model again using a previous job (spt13 showed an error message, but spt10 didn't) as a reference model. Now, I am trying e2spt_refine_new.py with the new initial model in a continuous build. I hope it passes the problem..

(/opt/e2test) [eman_test@lsb01 1xb_eman]$ e2iminfo.py --all --stat particles3d/NC4bx1_ali__a192ctf.hdf

particles3d/NC4bx1_ali__a192ctf.hdf 220 images in HDF5 format (swap) 192 x 192 x 192

0. apix=2.30 min=-4.257 max=4.239 mean=0.002038 sigma=0.9999 skewness=0.003046 kurtosis=0.2493 moment_inertia=2.364e+10 radius_gyration= 91.92
1. apix=2.30 min=-4.259 max=4.292 mean=0.001135 sigma=0.9999 skewness=0.004149 kurtosis=0.2622 moment_inertia=2.366e+10 radius_gyration= 92.01
2. apix=2.30 min=-4.27 max=4.253 mean=-0.006298 sigma=0.9999 skewness=0.0035 kurtosis=0.2608 moment_inertia= 2.34e+10 radius_gyration= 91.95
3. apix=2.30 min=-4.278 max=4.293 mean=0.007239 sigma=0.9999 skewness=0.008339 kurtosis=0.2657 moment_inertia=2.378e+10 radius_gyration= 91.91
4. apix=2.30 min=-4.309 max=4.3 mean=0.0004192 sigma=0.9999 skewness=0.004611 kurtosis=0.2618 moment_inertia=2.361e+10 radius_gyration= 91.97
5. apix=2.30 min=-4.279 max=4.276 mean=0.009251 sigma=0.9999 skewness=0.002944 kurtosis=0.2644 moment_inertia= 2.39e+10 radius_gyration= 92.02
6. apix=2.30 min=-4.267 max=4.215 mean=-0.004333 sigma=0.9999 skewness=-0.001203 kurtosis=0.2503 moment_inertia=2.357e+10 radius_gyration= 92.16
7. apix=2.30 min=-4.266 max=4.276 mean=0.007954 sigma=0.9999 skewness=-0.00155 kurtosis=0.2581 moment_inertia=2.394e+10 radius_gyration= 92.16
8. apix=2.30 min=-4.211 max=4.32 mean=0.001109 sigma=0.9999 skewness=0.009896 kurtosis=0.2619 moment_inertia=2.362e+10 radius_gyration= 91.95
9. apix=2.30 min=-4.249 max=4.288 mean=0.008715 sigma=0.9999 skewness=0.002381 kurtosis=0.2637 moment_inertia=2.393e+10 radius_gyration= 92.1
10. apix=2.30 min=-4.274 max=4.317 mean=-0.003295 sigma=0.9999 skewness=0.00725 kurtosis=0.263 moment_inertia=2.348e+10 radius_gyration= 91.93
11. apix=2.30 min=-4.308 max=4.302 mean=0.00323 sigma=0.9999 skewness=0.001892 kurtosis=0.2591 moment_inertia=2.377e+10 radius_gyration= 92.11
12. apix=2.30 min=-4.267 max=4.293 mean=0.004896 sigma=0.9999 skewness=0.009976 kurtosis=0.2649 moment_inertia= 2.37e+10 radius_gyration= 91.9
13. apix=2.30 min=-4.275 max=4.275 mean=-0.001386 sigma=0.9999 skewness=0.0005409 kurtosis=0.2556 moment_inertia=2.358e+10 radius_gyration= 92.01
14. apix=2.30 min=-4.314 max=4.22 mean=-0.00973 sigma=0.9999 skewness=0.0005084 kurtosis=0.2561 moment_inertia=2.326e+10 radius_gyration= 91.86
15. apix=2.30 min=-4.237 max=4.273 mean=-0.00625 sigma=0.9999 skewness=0.00267 kurtosis=0.2519 moment_inertia=2.346e+10 radius_gyration= 92.07
16. apix=2.30 min=-4.275 max=4.237 mean=-0.006939 sigma=0.9999 skewness=-0.0009039 kurtosis=0.243 moment_inertia=2.347e+10 radius_gyration= 92.09
17. apix=2.30 min=-4.275 max=4.238 mean=0.008423 sigma=0.9999 skewness=0.003444 kurtosis=0.2568 moment_inertia=2.388e+10 radius_gyration= 92.02
18. apix=2.30 min=-4.262 max=4.281 mean=0.002881 sigma=0.9999 skewness=0.002977 kurtosis=0.2561 moment_inertia=2.371e+10 radius_gyration= 92.01
19. apix=2.30 min=-4.233 max=4.312 mean=-0.003196 sigma=0.9999 skewness=0.002111 kurtosis=0.2548 moment_inertia=2.356e+10 radius_gyration= 92.08
20. apix=2.30 min=-4.22 max=4.261 mean=-0.004705 sigma=0.9999 skewness=0.006107 kurtosis=0.2617 moment_inertia=2.341e+10 radius_gyration= 91.87
21. apix=2.30 min=-4.264 max=4.231 mean=-0.002855 sigma=0.9999 skewness=-0.002854 kurtosis=0.2522 moment_inertia= 2.36e+10 radius_gyration= 92.13
22. apix=2.30 min=-4.257 max=4.292 mean=0.003075 sigma=0.9999 skewness=0.001949 kurtosis=0.2619 moment_inertia= 2.37e+10 radius_gyration= 91.99
23. apix=2.30 min=-4.226 max=4.319 mean=0.01018 sigma=0.9999 skewness=0.007521 kurtosis=0.2589 moment_inertia=2.394e+10 radius_gyration= 92.04
24. apix=2.30 min=-4.241 max=4.31 mean=-0.005849 sigma=0.9999 skewness=0.003729 kurtosis=0.2585 moment_inertia=2.338e+10 radius_gyration= 91.88
25. apix=2.30 min=-4.261 max=4.276 mean=-0.001945 sigma=0.9999 skewness=0.003476 kurtosis=0.2596 moment_inertia=2.356e+10 radius_gyration= 92
26. apix=2.30 min=-4.26 max=4.3 mean=0.007089 sigma=0.9999 skewness=0.005309 kurtosis=0.2544 moment_inertia=2.381e+10 radius_gyration= 91.96
27. apix=2.30 min=-4.26 max=4.284 mean=0.001423 sigma=0.9999 skewness=-0.001688 kurtosis=0.2517 moment_inertia=2.373e+10 radius_gyration= 92.13
28. apix=2.30 min=-4.273 max=4.258 mean=-0.006622 sigma=0.9999 skewness=0.0005066 kurtosis=0.2593 moment_inertia=2.343e+10 radius_gyration= 92.02
29. apix=2.30 min=-4.225 max=4.281 mean=0.008371 sigma=0.9999 skewness=0.005149 kurtosis=0.2522 moment_inertia=2.388e+10 radius_gyration= 92
30. apix=2.30 min=-4.246 max=4.286 mean=0.007778 sigma=0.9999 skewness=-7.079e-05 kurtosis=0.2535 moment_inertia=2.393e+10 radius_gyration= 92.14
31. apix=2.30 min=-4.278 max=4.273 mean=0.003932 sigma=0.9999 skewness=-0.001604 kurtosis=0.2499 moment_inertia=2.384e+10 radius_gyration= 92.17
32. apix=2.30 min=-4.271 max=4.273 mean=0.004274 sigma=0.9999 skewness=0.0004167 kurtosis=0.2644 moment_inertia=2.382e+10 radius_gyration= 92.16
33. apix=2.30 min=-4.25 max=4.29 mean=0.002722 sigma=0.9999 skewness=0.005178 kurtosis=0.2654 moment_inertia=2.368e+10 radius_gyration= 91.98
34. apix=2.30 min=-4.235 max=4.272 mean=0.009887 sigma=0.9999 skewness=0.002385 kurtosis=0.2553 moment_inertia=2.394e+10 radius_gyration= 92.05
35. apix=2.30 min=-4.25 max=4.226 mean=-0.003483 sigma=0.9999 skewness=-0.002811 kurtosis=0.2498 moment_inertia=2.365e+10 radius_gyration= 92.24
36. apix=2.30 min=-4.251 max=4.263 mean=0.01333 sigma=0.9999 skewness=0.005897 kurtosis=0.2538 moment_inertia=2.404e+10 radius_gyration= 92.03
37. apix=2.30 min=-4.255 max=4.258 mean=-0.005924 sigma=0.9999 skewness=0.002059 kurtosis=0.2534 moment_inertia=2.347e+10 radius_gyration= 92.05
38. apix=2.30 min=-4.253 max=4.335 mean=0.007138 sigma=0.9999 skewness=0.003226 kurtosis=0.2635 moment_inertia=2.392e+10 radius_gyration= 92.17
39. apix=2.30 min=-4.216 max=4.27 mean=-0.001975 sigma=0.9999 skewness=0.007901 kurtosis=0.2437 moment_inertia=2.356e+10 radius_gyration= 91.97
40. apix=2.30 min=-4.259 max=4.268 mean=-0.003242 sigma=0.9999 skewness=-0.002259 kurtosis=0.2567 moment_inertia= 2.36e+10 radius_gyration= 92.16
41. apix=2.30 min=-4.275 max=4.267 mean=0.003228 sigma=0.9999 skewness=0.008849 kurtosis=0.2498 moment_inertia=2.376e+10 radius_gyration= 92.06
42. apix=2.30 min=-4.265 max=4.334 mean=0.01159 sigma=0.9999 skewness=0.009188 kurtosis=0.2645 moment_inertia=2.395e+10 radius_gyration= 91.98
43. apix=2.30 min=-4.274 max=4.271 mean=8.895e-06 sigma=0.9999 skewness=0.004061 kurtosis=0.2568 moment_inertia=2.365e+10 radius_gyration= 92.05
44. apix=2.30 min=-4.281 max=4.306 mean=0.005798 sigma=0.9999 skewness=0.009944 kurtosis=0.2655 moment_inertia=2.375e+10 radius_gyration= 91.92
45. apix=2.30 min=-4.219 max=4.333 mean=-0.002576 sigma=0.9999 skewness=0.008074 kurtosis=0.2549 moment_inertia=2.356e+10 radius_gyration= 92.03
46. apix=2.30 min=-4.267 max=4.237 mean=-0.003455 sigma=0.9999 skewness=-0.003308 kurtosis=0.2492 moment_inertia= 2.36e+10 radius_gyration= 92.15
47. apix=2.30 min=-4.22 max=4.279 mean=0.0009963 sigma=0.9999 skewness=0.01009 kurtosis=0.2535 moment_inertia=2.365e+10 radius_gyration= 92
48. apix=2.30 min=-4.22 max=4.328 mean=0.003124 sigma=0.9999 skewness=0.005947 kurtosis=0.2595 moment_inertia=2.375e+10 radius_gyration= 92.07
49. apix=2.30 min=-4.269 max=4.263 mean=-0.003634 sigma=0.9999 skewness=0.002879 kurtosis=0.2543 moment_inertia=2.354e+10 radius_gyration= 92.05
50. apix=2.30 min=-4.256 max=4.274 mean=0.003679 sigma=0.9999 skewness=0.002437 kurtosis=0.2511 moment_inertia=2.383e+10 radius_gyration= 92.18
51. apix=2.30 min=-4.255 max=4.262 mean=0.007679 sigma=0.9999 skewness=0.002985 kurtosis=0.252 moment_inertia=2.385e+10 radius_gyration= 92.01
52. apix=2.30 min=-4.226 max=4.263 mean=-0.004421 sigma=0.9999 skewness=0.004635 kurtosis=0.2592 moment_inertia=2.348e+10 radius_gyration= 92
53. apix=2.30 min=-4.222 max=4.301 mean=0.004845 sigma=0.9999 skewness=0.006202 kurtosis=0.254 moment_inertia=2.373e+10 radius_gyration= 91.93
54. apix=2.30 min=-4.309 max=4.285 mean=0.003139 sigma=0.9999 skewness=0.003824 kurtosis=0.2619 moment_inertia=2.374e+10 radius_gyration= 92.05
55. apix=2.30 min=-4.233 max=4.28 mean=-0.0098 sigma=0.9999 skewness=0.003954 kurtosis=0.2524 moment_inertia=2.333e+10 radius_gyration= 91.98
56. apix=2.30 min=-4.234 max=4.308 mean=0.01235 sigma=0.9999 skewness=0.0067 kurtosis=0.2595 moment_inertia=2.398e+10 radius_gyration= 91.98
57. apix=2.30 min=-4.26 max=4.244 mean=0.004963 sigma=0.9999 skewness=0.004403 kurtosis=0.2556 moment_inertia=2.377e+10 radius_gyration= 92
58. apix=2.30 min=-4.239 max=4.296 mean=-0.0001606 sigma=0.9999 skewness=0.004874 kurtosis=0.2548 moment_inertia=2.359e+10 radius_gyration= 91.95
59. apix=2.30 min=-4.274 max=4.345 mean=-4.692e-05 sigma=0.9999 skewness=0.006146 kurtosis=0.2685 moment_inertia= 2.36e+10 radius_gyration= 91.98
60. apix=2.30 min=-4.284 max=4.263 mean=-0.003278 sigma=0.9999 skewness=0.001425 kurtosis=0.2581 moment_inertia=2.349e+10 radius_gyration= 91.94
61. apix=2.30 min=-4.245 max=4.256 mean=0.000414 sigma=0.9999 skewness=0.001127 kurtosis=0.2574 moment_inertia=2.365e+10 radius_gyration= 92.04
62. apix=2.30 min=-4.268 max=4.27 mean=-0.00258 sigma=0.9999 skewness=0.001928 kurtosis=0.2631 moment_inertia=2.354e+10 radius_gyration= 92.01
63. apix=2.30 min=-4.231 max=4.256 mean=0.003113 sigma=0.9999 skewness=0.005512 kurtosis=0.2441 moment_inertia=2.377e+10 radius_gyration= 92.08
64. apix=2.30 min=-4.233 max=4.302 mean=-0.0007897 sigma=0.9999 skewness=0.007202 kurtosis=0.2556 moment_inertia= 2.36e+10 radius_gyration= 92
65. apix=2.30 min=-4.253 max=4.288 mean=0.005243 sigma=0.9999 skewness=0.007186 kurtosis=0.2546 moment_inertia=2.377e+10 radius_gyration= 91.99
66. apix=2.30 min=-4.255 max=4.269 mean=0.002615 sigma=0.9999 skewness=0.002146 kurtosis=0.2597 moment_inertia=2.373e+10 radius_gyration= 92.07
67. apix=2.30 min=-4.236 max=4.281 mean=0.01232 sigma=0.9999 skewness=0.00566 kurtosis=0.2529 moment_inertia= 2.4e+10 radius_gyration= 92.01
68. apix=2.30 min=-4.257 max=4.326 mean=0.006651 sigma=0.9999 skewness=0.008232 kurtosis=0.2545 moment_inertia=2.384e+10 radius_gyration= 92.04
69. apix=2.30 min=-4.27 max=4.254 mean=-0.002914 sigma=0.9999 skewness=0.002972 kurtosis=0.2574 moment_inertia=2.355e+10 radius_gyration= 92.04
70. apix=2.30 min=-4.26 max=4.293 mean=-0.0005195 sigma=0.9999 skewness=0.007147 kurtosis=0.26 moment_inertia=2.362e+10 radius_gyration= 92.05
71. apix=2.30 min=-4.285 max=4.282 mean=-0.007438 sigma=0.9999 skewness=0.002285 kurtosis=0.2513 moment_inertia= 2.34e+10 radius_gyration= 91.99
72. apix=2.30 min=-4.264 max=4.27 mean=0.004272 sigma=0.9999 skewness=0.003143 kurtosis=0.2559 moment_inertia=2.377e+10 radius_gyration= 92.04
73. apix=2.30 min=-4.283 max=4.29 mean=0.00851 sigma=0.9999 skewness=0.003888 kurtosis=0.2539 moment_inertia= 2.39e+10 radius_gyration= 92.04
74. apix=2.30 min=-4.247 max=4.323 mean=0.005008 sigma=0.9999 skewness=0.0008247 kurtosis=0.2566 moment_inertia=2.382e+10 radius_gyration= 92.09
75. apix=2.30 min=-4.265 max=4.314 mean=0.009654 sigma=0.9999 skewness=0.004963 kurtosis=0.2691 moment_inertia=2.387e+10 radius_gyration= 91.95
76. apix=2.30 min=-4.241 max=4.242 mean=0.003773 sigma=0.9999 skewness=0.004948 kurtosis=0.2398 moment_inertia=2.378e+10 radius_gyration= 92.05
77. apix=2.30 min=-4.275 max=4.223 mean=0.000889 sigma=0.9999 skewness=0.0005068 kurtosis=0.2601 moment_inertia=2.366e+10 radius_gyration= 92.04
78. apix=2.30 min=-4.211 max=4.314 mean=0.009524 sigma=0.9999 skewness=0.005522 kurtosis=0.2574 moment_inertia=2.398e+10 radius_gyration= 92.15
79. apix=2.30 min=-4.289 max=4.314 mean=0.01005 sigma=0.9999 skewness=0.004102 kurtosis=0.2684 moment_inertia=2.389e+10 radius_gyration= 91.96
80. apix=2.30 min=-4.25 max=4.297 mean=0.005522 sigma=0.9999 skewness=0.003613 kurtosis=0.2635 moment_inertia=2.378e+10 radius_gyration= 92
81. apix=2.30 min=-4.229 max=4.308 mean=0.003403 sigma=0.9999 skewness=0.003941 kurtosis=0.2651 moment_inertia=2.371e+10 radius_gyration= 92
82. apix=2.30 min=-4.249 max=4.276 mean=-0.002135 sigma=0.9999 skewness=0.002841 kurtosis=0.2516 moment_inertia=2.351e+10 radius_gyration= 91.91
83. apix=2.30 min=-4.263 max=4.259 mean=0.006275 sigma=0.9999 skewness=0.004906 kurtosis=0.2462 moment_inertia=2.386e+10 radius_gyration= 92.07
84. apix=2.30 min=-4.291 max=4.299 mean=0.004321 sigma=0.9999 skewness=0.004943 kurtosis=0.2676 moment_inertia=2.373e+10 radius_gyration= 91.97
85. apix=2.30 min=-4.271 max=4.265 mean=0.00632 sigma=0.9999 skewness=-0.001301 kurtosis=0.2585 moment_inertia=2.385e+10 radius_gyration= 92.09
86. apix=2.30 min=-4.299 max=4.311 mean=0.002388 sigma=0.9999 skewness=0.006925 kurtosis=0.265 moment_inertia=2.365e+10 radius_gyration= 91.94
87. apix=2.30 min=-4.272 max=4.312 mean=0.001806 sigma=0.9999 skewness=0.003368 kurtosis=0.2601 moment_inertia=2.369e+10 radius_gyration= 92.03
88. apix=2.30 min=-4.223 max=4.293 mean=-0.002391 sigma=0.9999 skewness=-7.338e-05 kurtosis=0.2457 moment_inertia=2.363e+10 radius_gyration= 92.13
89. apix=2.30 min=-4.268 max=4.285 mean=-0.002352 sigma=0.9999 skewness=0.004481 kurtosis=0.2572 moment_inertia=2.353e+10 radius_gyration= 91.98
90. apix=2.30 min=-4.265 max=4.258 mean=0.002882 sigma=0.9999 skewness=0.00171 kurtosis=0.2611 moment_inertia=2.372e+10 radius_gyration= 92.03
91. apix=2.30 min=-4.236 max=4.266 mean=0.009042 sigma=0.9999 skewness=0.001401 kurtosis=0.2564 moment_inertia=2.392e+10 radius_gyration= 92.06
92. apix=2.30 min=-4.281 max=4.317 mean=-0.002904 sigma=0.9999 skewness=0.009789 kurtosis=0.2744 moment_inertia=2.347e+10 radius_gyration= 91.91
93. apix=2.30 min=-4.234 max=4.302 mean=0.006344 sigma=0.9999 skewness=0.004629 kurtosis=0.249 moment_inertia=2.388e+10 radius_gyration= 92.11
94. apix=2.30 min=-4.362 max=4.293 mean=-0.003984 sigma=0.9999 skewness=-0.003133 kurtosis=0.2633 moment_inertia=2.354e+10 radius_gyration= 92.08
95. apix=2.30 min=-4.284 max=4.293 mean=-0.009425 sigma=0.9999 skewness=0.00326 kurtosis=0.262 moment_inertia=2.332e+10 radius_gyration= 91.96
96. apix=2.30 min=-4.236 max=4.259 mean=0.003994 sigma=0.9999 skewness=-0.0004863 kurtosis=0.2493 moment_inertia=2.379e+10 radius_gyration= 92.1
97. apix=2.30 min=-4.302 max=4.232 mean=-0.008192 sigma=0.9999 skewness=0.001048 kurtosis=0.2563 moment_inertia=2.339e+10 radius_gyration= 92.02
98. apix=2.30 min=-4.315 max=4.248 mean=0.00555 sigma=0.9999 skewness=-0.002738 kurtosis=0.2535 moment_inertia=2.382e+10 radius_gyration= 92.06
99. apix=2.30 min=-4.23 max=4.271 mean=0.008051 sigma=0.9999 skewness=0.003142 kurtosis=0.2535 moment_inertia=2.393e+10 radius_gyration= 92.12
100. apix=2.30 min=-4.229 max=4.203 mean=-0.001729 sigma=0.9999 skewness=0.002692 kurtosis=0.2458 moment_inertia= 2.36e+10 radius_gyration= 92.04
101. apix=2.30 min=-4.237 max=4.328 mean=0.008005 sigma=0.9999 skewness=0.01044 kurtosis=0.2638 moment_inertia=2.381e+10 radius_gyration= 91.94
102. apix=2.30 min=-4.247 max=4.3 mean=-0.0006379 sigma=0.9999 skewness=0.00988 kurtosis=0.2522 moment_inertia= 2.36e+10 radius_gyration= 91.98
103. apix=2.30 min=-4.241 max=4.303 mean=0.009481 sigma=0.9999 skewness=0.00643 kurtosis=0.2478 moment_inertia=2.396e+10 radius_gyration= 92.08
104. apix=2.30 min=-4.304 max=4.311 mean=-0.001282 sigma=0.9999 skewness=-0.00138 kurtosis=0.267 moment_inertia=2.362e+10 radius_gyration= 92.08
105. apix=2.30 min=-4.248 max=4.309 mean=-0.00104 sigma=0.9999 skewness=0.004568 kurtosis=0.2565 moment_inertia=2.362e+10 radius_gyration= 92.06
106. apix=2.30 min=-4.236 max=4.33 mean=0.003599 sigma=0.9999 skewness=0.003369 kurtosis=0.2542 moment_inertia=2.377e+10 radius_gyration= 92.07
107. apix=2.30 min=-4.251 max=4.254 mean=0.004297 sigma=0.9999 skewness=-0.003088 kurtosis=0.2429 moment_inertia=2.386e+10 radius_gyration= 92.19
108. apix=2.30 min=-4.223 max=4.279 mean=5.233e-05 sigma=0.9999 skewness=0.002005 kurtosis=0.2595 moment_inertia=2.365e+10 radius_gyration= 92.06
109. apix=2.30 min=-4.27 max=4.293 mean=0.001608 sigma=0.9999 skewness=0.005076 kurtosis=0.2705 moment_inertia=2.366e+10 radius_gyration= 92.01
110. apix=2.30 min=-4.298 max=4.259 mean=0.003625 sigma=0.9999 skewness=0.004229 kurtosis=0.2663 moment_inertia=2.374e+10 radius_gyration= 92.05
111. apix=2.30 min=-4.251 max=4.3 mean=0.001436 sigma=0.9999 skewness=0.007842 kurtosis=0.2603 moment_inertia=2.364e+10 radius_gyration= 91.96
112. apix=2.30 min=-4.237 max=4.302 mean=-0.001403 sigma=0.9999 skewness=0.007473 kurtosis=0.2661 moment_inertia=2.352e+10 radius_gyration= 91.91
113. apix=2.30 min=-4.251 max=4.31 mean=-0.006386 sigma=0.9999 skewness=0.001127 kurtosis=0.2564 moment_inertia=2.354e+10 radius_gyration= 92.21
114. apix=2.30 min=-4.247 max=4.255 mean=0.006589 sigma=0.9999 skewness=0.002775 kurtosis=0.2421 moment_inertia=2.387e+10 radius_gyration= 92.08
115. apix=2.30 min=-4.23 max=4.292 mean=0.0008073 sigma=0.9999 skewness=0.002708 kurtosis=0.2581 moment_inertia=2.362e+10 radius_gyration= 91.95
116. apix=2.30 min=-4.279 max=4.262 mean=0.002409 sigma=0.9999 skewness=-0.001595 kurtosis=0.2604 moment_inertia= 2.38e+10 radius_gyration= 92.2
117. apix=2.30 min=-4.256 max=4.261 mean=0.0007954 sigma=0.9999 skewness=0.005007 kurtosis=0.2546 moment_inertia=2.362e+10 radius_gyration= 91.96
118. apix=2.30 min=-4.27 max=4.242 mean=0.01084 sigma=0.9999 skewness=-0.003293 kurtosis=0.2482 moment_inertia=2.409e+10 radius_gyration= 92.26
119. apix=2.30 min=-4.232 max=4.294 mean=-0.004469 sigma=0.9999 skewness=0.003595 kurtosis=0.2564 moment_inertia=2.349e+10 radius_gyration= 92
120. apix=2.30 min=-4.235 max=4.285 mean=0.0009341 sigma=0.9999 skewness=0.00299 kurtosis=0.2623 moment_inertia=2.367e+10 radius_gyration= 92.05
121. apix=2.30 min=-4.252 max=4.264 mean=-0.006107 sigma=0.9999 skewness=-0.0006824 kurtosis=0.2637 moment_inertia=2.349e+10 radius_gyration= 92.11
122. apix=2.30 min=-4.222 max=4.285 mean=0.005792 sigma=0.9999 skewness=0.0005343 kurtosis=0.2527 moment_inertia=2.389e+10 radius_gyration= 92.18
123. apix=2.30 min=-4.284 max=4.3 mean=0.01047 sigma=0.9999 skewness=0.003932 kurtosis=0.2628 moment_inertia=2.393e+10 radius_gyration= 92
124. apix=2.30 min=-4.241 max=4.271 mean=0.009947 sigma=0.9999 skewness=0.004325 kurtosis=0.2563 moment_inertia=2.399e+10 radius_gyration= 92.13
125. apix=2.30 min=-4.263 max=4.254 mean=0.004064 sigma=0.9999 skewness=0.006707 kurtosis=0.2618 moment_inertia=2.367e+10 radius_gyration= 91.88
126. apix=2.30 min=-4.254 max=4.242 mean=0.003707 sigma=0.9999 skewness=-0.001236 kurtosis=0.2456 moment_inertia=2.382e+10 radius_gyration= 92.16
127. apix=2.30 min=-4.281 max=4.251 mean=0.0005657 sigma=0.9999 skewness=-0.001762 kurtosis=0.2625 moment_inertia=2.367e+10 radius_gyration= 92.09
128. apix=2.30 min=-4.251 max=4.295 mean=-0.003442 sigma=0.9999 skewness=0.003639 kurtosis=0.2634 moment_inertia=2.352e+10 radius_gyration= 92.02
129. apix=2.30 min=-4.272 max=4.274 mean=-0.001481 sigma=0.9999 skewness=0.001148 kurtosis=0.2664 moment_inertia=2.358e+10 radius_gyration= 92.01
130. apix=2.30 min=-4.298 max=4.255 mean=-0.005408 sigma=0.9999 skewness=0.003105 kurtosis=0.2617 moment_inertia=2.343e+10 radius_gyration= 91.96
131. apix=2.30 min=-4.265 max=4.282 mean=0.005528 sigma=0.9999 skewness=0.001389 kurtosis=0.2608 moment_inertia=2.384e+10 radius_gyration= 92.12
132. apix=2.30 min=-4.257 max=4.306 mean=0.004736 sigma=0.9999 skewness=0.00584 kurtosis=0.2559 moment_inertia=2.382e+10 radius_gyration= 92.11
133. apix=2.30 min=-4.24 max=4.266 mean=5.492e-05 sigma=0.9999 skewness=0.0001907 kurtosis=0.2526 moment_inertia=2.366e+10 radius_gyration= 92.07
134. apix=2.30 min=-4.209 max=4.284 mean=0.007256 sigma=0.9999 skewness=0.006986 kurtosis=0.2503 moment_inertia=2.387e+10 radius_gyration= 92.06
135. apix=2.30 min=-4.262 max=4.273 mean=-0.01399 sigma=0.9999 skewness=-0.0005846 kurtosis=0.2659 moment_inertia=2.318e+10 radius_gyration= 91.96
136. apix=2.30 min=-4.241 max=4.302 mean=0.009269 sigma=0.9999 skewness=0.005719 kurtosis=0.2618 moment_inertia=2.392e+10 radius_gyration= 92.06
137. apix=2.30 min=-4.228 max=4.249 mean=-0.008132 sigma=0.9999 skewness=0.004106 kurtosis=0.2557 moment_inertia=2.336e+10 radius_gyration= 91.97
138. apix=2.30 min=-4.226 max=4.279 mean=0.003063 sigma=0.9999 skewness=0.001723 kurtosis=0.2576 moment_inertia=2.377e+10 radius_gyration= 92.11
139. apix=2.30 min=-4.18 max=4.241 mean=0.004966 sigma=0.9999 skewness=0.006186 kurtosis=0.2516 moment_inertia=2.379e+10 radius_gyration= 92.05
140. apix=2.30 min=-4.233 max=4.263 mean=-0.003353 sigma=0.9999 skewness=0.006341 kurtosis=0.255 moment_inertia=2.353e+10 radius_gyration= 92.01
141. apix=2.30 min=-4.309 max=4.275 mean=-0.0102 sigma=0.9999 skewness=-0.001864 kurtosis=0.2697 moment_inertia=2.332e+10 radius_gyration= 92.03
142. apix=2.30 min=-4.284 max=4.301 mean=0.01043 sigma=0.9999 skewness=0.009444 kurtosis=0.2683 moment_inertia=2.388e+10 radius_gyration= 91.92
143. apix=2.30 min=-4.259 max=4.307 mean=-0.003443 sigma=0.9999 skewness=0.001266 kurtosis=0.2627 moment_inertia=2.355e+10 radius_gyration= 92.08
144. apix=2.30 min=-4.243 max=4.274 mean=0.0001648 sigma=0.9999 skewness=0.003947 kurtosis=0.2599 moment_inertia=2.359e+10 radius_gyration= 91.94
145. apix=2.30 min=-4.234 max=4.259 mean=-0.001443 sigma=0.9999 skewness=0.000289 kurtosis=0.2545 moment_inertia=2.364e+10 radius_gyration= 92.13
146. apix=2.30 min=-4.277 max=4.236 mean=-0.001399 sigma=0.9999 skewness=-0.002468 kurtosis=0.2518 moment_inertia=2.368e+10 radius_gyration= 92.18
147. apix=2.30 min=-4.227 max=4.279 mean=0.01283 sigma=0.9999 skewness=0.0004307 kurtosis=0.2479 moment_inertia=2.404e+10 radius_gyration= 92.05
148. apix=2.30 min=-4.27 max=4.281 mean=-0.003389 sigma=0.9999 skewness=-0.0005751 kurtosis=0.2522 moment_inertia=2.364e+10 radius_gyration= 92.24
149. apix=2.30 min=-4.283 max=4.253 mean=-0.003994 sigma=0.9999 skewness=0.0008841 kurtosis=0.2558 moment_inertia=2.354e+10 radius_gyration= 92.08
150. apix=2.30 min=-4.303 max=4.264 mean=-0.00391 sigma=0.9999 skewness=0.001387 kurtosis=0.2561 moment_inertia=2.351e+10 radius_gyration= 92.02
151. apix=2.30 min=-4.295 max=4.255 mean=0.002992 sigma=0.9999 skewness=0.002088 kurtosis=0.2573 moment_inertia=2.376e+10 radius_gyration= 92.11
152. apix=2.30 min=-4.288 max=4.286 mean=0.003962 sigma=0.9999 skewness=-0.001422 kurtosis=0.2664 moment_inertia=2.382e+10 radius_gyration= 92.18
153. apix=2.30 min=-4.262 max=4.238 mean=-0.002878 sigma=0.9999 skewness=1.014e-05 kurtosis=0.2574 moment_inertia=2.361e+10 radius_gyration= 92.16
154. apix=2.30 min=-4.256 max=4.274 mean=0.005555 sigma=0.9999 skewness=0.00358 kurtosis=0.2492 moment_inertia=2.386e+10 radius_gyration= 92.13
155. apix=2.30 min=-4.288 max=4.3 mean=0.002554 sigma=0.9999 skewness=0.003169 kurtosis=0.2593 moment_inertia=2.378e+10 radius_gyration= 92.17
156. apix=2.30 min=-4.27 max=4.278 mean=-0.003572 sigma=0.9999 skewness=0.00137 kurtosis=0.2548 moment_inertia=2.355e+10 radius_gyration= 92.08
157. apix=2.30 min=-4.253 max=4.286 mean=-0.00536 sigma=0.9999 skewness=0.005244 kurtosis=0.267 moment_inertia=2.343e+10 radius_gyration= 91.96
158. apix=2.30 min=-4.274 max=4.264 mean=0.006336 sigma=0.9999 skewness=-0.001474 kurtosis=0.2552 moment_inertia=2.386e+10 radius_gyration= 92.1
159. apix=2.30 min=-4.256 max=4.293 mean=0.008936 sigma=0.9999 skewness=0.001633 kurtosis=0.2553 moment_inertia= 2.39e+10 radius_gyration= 92.03
160. apix=2.30 min=-4.292 max=4.254 mean=0.001026 sigma=0.9999 skewness=-0.002565 kurtosis=0.2668 moment_inertia=2.362e+10 radius_gyration= 91.96
161. apix=2.30 min=-4.239 max=4.25 mean=-0.006042 sigma=0.9999 skewness=0.004106 kurtosis=0.26 moment_inertia=2.343e+10 radius_gyration= 92
162. apix=2.30 min=-4.276 max=4.28 mean=-0.001977 sigma=0.9999 skewness=0.002798 kurtosis=0.2546 moment_inertia=2.362e+10 radius_gyration= 92.11
163. apix=2.30 min=-4.282 max=4.27 mean=-0.01139 sigma=0.9999 skewness=-0.0003818 kurtosis=0.2593 moment_inertia=2.335e+10 radius_gyration= 92.13
164. apix=2.30 min=-4.317 max=4.253 mean=-0.009048 sigma=0.9999 skewness=-0.004132 kurtosis=0.2639 moment_inertia=2.343e+10 radius_gyration= 92.17
165. apix=2.30 min=-4.251 max=4.234 mean=0.001492 sigma=0.9999 skewness=-0.001569 kurtosis=0.249 moment_inertia=2.384e+10 radius_gyration= 92.33
166. apix=2.30 min=-4.326 max=4.226 mean=-0.006249 sigma=0.9999 skewness=-0.0006017 kurtosis=0.2489 moment_inertia=2.351e+10 radius_gyration= 92.13
167. apix=2.30 min=-4.254 max=4.288 mean=0.007887 sigma=0.9999 skewness=0.00125 kurtosis=0.2698 moment_inertia=2.381e+10 radius_gyration= 91.94
168. apix=2.30 min=-4.314 max=4.254 mean=-0.002784 sigma=0.9999 skewness=0.0008077 kurtosis=0.2666 moment_inertia=2.356e+10 radius_gyration= 92.07
169. apix=2.30 min=-4.29 max=4.289 mean=0.003704 sigma=0.9999 skewness=0.002341 kurtosis=0.2598 moment_inertia=2.377e+10 radius_gyration= 92.07
170. apix=2.30 min=-4.253 max=4.323 mean=0.001307 sigma=0.9999 skewness=0.01368 kurtosis=0.2676 moment_inertia=2.376e+10 radius_gyration= 92.21
171. apix=2.30 min=-4.256 max=4.256 mean=-0.007264 sigma=0.9999 skewness=-0.0006805 kurtosis=0.2417 moment_inertia=2.351e+10 radius_gyration= 92.17
172. apix=2.30 min=-4.296 max=4.303 mean=0.006884 sigma=0.9999 skewness=0.002998 kurtosis=0.2668 moment_inertia=2.386e+10 radius_gyration= 92.08
173. apix=2.30 min=-4.266 max=4.277 mean=-0.003208 sigma=0.9999 skewness=-0.0005261 kurtosis=0.258 moment_inertia=2.354e+10 radius_gyration= 92.04
174. apix=2.30 min=-4.253 max=4.28 mean=-0.0007801 sigma=0.9999 skewness=0.002232 kurtosis=0.2599 moment_inertia=2.362e+10 radius_gyration= 92.07
175. apix=2.30 min=-4.253 max=4.278 mean=0.01087 sigma=0.9999 skewness=0.001668 kurtosis=0.2534 moment_inertia= 2.4e+10 radius_gyration= 92.1
176. apix=2.30 min=-4.265 max=4.274 mean=0.005784 sigma=0.9999 skewness=-0.003123 kurtosis=0.2569 moment_inertia=2.386e+10 radius_gyration= 92.14
177. apix=2.30 min=-4.272 max=4.287 mean=0.006025 sigma=0.9999 skewness=0.000472 kurtosis=0.2508 moment_inertia=2.388e+10 radius_gyration= 92.14
178. apix=2.30 min=-4.265 max=4.274 mean=0.00028 sigma=0.9999 skewness=-0.0001322 kurtosis=0.2538 moment_inertia=2.373e+10 radius_gyration= 92.19
179. apix=2.30 min=-4.2 max=4.683 mean=0.01916 sigma=0.9999 skewness=0.0691 kurtosis=0.392 moment_inertia=2.397e+10 radius_gyration= 91.77
180. apix=2.30 min=-4.238 max=4.248 mean=0.0002645 sigma=0.9999 skewness=-0.001318 kurtosis=0.2507 moment_inertia=2.368e+10 radius_gyration= 92.09
181. apix=2.30 min=-4.253 max=4.303 mean=0.006574 sigma=0.9999 skewness=0.005112 kurtosis=0.2475 moment_inertia= 2.39e+10 radius_gyration= 92.15
182. apix=2.30 min=-4.208 max=4.31 mean=-0.009607 sigma=0.9999 skewness=0.01972 kurtosis=0.263 moment_inertia=2.341e+10 radius_gyration= 92.16
183. apix=2.30 min=-4.153 max=4.56 mean=0.01757 sigma=0.9999 skewness=0.04614 kurtosis=0.318 moment_inertia= 2.43e+10 radius_gyration= 92.39
184. apix=2.30 min=-4.294 max=4.266 mean=0.002183 sigma=0.9999 skewness=-0.006571 kurtosis=0.2548 moment_inertia=2.379e+10 radius_gyration= 92.21
185. apix=2.30 min=-4.283 max=4.258 mean=-0.008515 sigma=0.9999 skewness=-0.005047 kurtosis=0.2528 moment_inertia=2.344e+10 radius_gyration= 92.13
186. apix=2.30 min=-4.268 max=4.258 mean=-0.0003051 sigma=0.9999 skewness=-0.001055 kurtosis=0.2499 moment_inertia=2.364e+10 radius_gyration= 92.04
187. apix=2.30 min=-4.331 max=4.229 mean=-0.0049 sigma=0.9999 skewness=-0.00393 kurtosis=0.2638 moment_inertia=2.352e+10 radius_gyration= 92.12
188. apix=2.30 min=-4.28 max=4.261 mean=-0.006867 sigma=0.9999 skewness=-0.001845 kurtosis=0.2506 moment_inertia=2.347e+10 radius_gyration= 92.11
189. apix=2.30 min=-4.286 max=4.888 mean=0.003087 sigma=0.9999 skewness=0.02966 kurtosis=0.3364 moment_inertia=2.358e+10 radius_gyration= 91.82
190. apix=2.30 min=-4.249 max=4.259 mean=0.004654 sigma=0.9999 skewness=0.0003472 kurtosis=0.2535 moment_inertia=2.385e+10 radius_gyration= 92.18
191. apix=2.30 min=-4.228 max=4.311 mean=0.003857 sigma=0.9999 skewness=0.005583 kurtosis=0.2525 moment_inertia=2.374e+10 radius_gyration= 92
192. apix=2.30 min=-4.245 max=4.308 mean=0.003762 sigma=0.9999 skewness=0.003423 kurtosis=0.2689 moment_inertia= 2.38e+10 radius_gyration= 92.15
193. apix=2.30 min=-4.306 max=4.286 mean=0.001534 sigma=0.9999 skewness=-0.000905 kurtosis=0.2613 moment_inertia=2.371e+10 radius_gyration= 92.09
194. apix=2.30 min=-4.313 max=4.293 mean=0.00024 sigma=0.9999 skewness=0.001138 kurtosis=0.2666 moment_inertia=2.362e+10 radius_gyration= 92.01
195. apix=2.30 min=-4.282 max=4.302 mean=0.009351 sigma=0.9999 skewness=0.003488 kurtosis=0.2626 moment_inertia=2.396e+10 radius_gyration= 92.12
196. apix=2.30 min=-4.211 max=4.32 mean=0.01831 sigma=0.9999 skewness=0.006847 kurtosis=0.2629 moment_inertia=2.415e+10 radius_gyration= 91.97
197. apix=2.30 min=-4.227 max=4.273 mean=-0.003126 sigma=0.9999 skewness=0.006524 kurtosis=0.2463 moment_inertia=2.359e+10 radius_gyration= 92.11
198. apix=2.30 min=-4.257 max=4.314 mean=0.00586 sigma=0.9999 skewness=-0.00319 kurtosis=0.2576 moment_inertia=2.394e+10 radius_gyration= 92.29
199. apix=2.30 min=-4.261 max=4.288 mean=0.005754 sigma=0.9999 skewness=-0.0009623 kurtosis=0.2626 moment_inertia=2.392e+10 radius_gyration= 92.26
200. apix=2.30 min=-4.272 max=4.273 mean=0.005472 sigma=0.9999 skewness=-0.0004025 kurtosis=0.2583 moment_inertia= 2.38e+10 radius_gyration= 92.04
201. apix=2.30 min=-4.283 max=4.243 mean=-0.002657 sigma=0.9999 skewness=0.004142 kurtosis=0.2539 moment_inertia=2.359e+10 radius_gyration= 92.1
202. apix=2.30 min=-4.265 max=4.261 mean=0.004938 sigma=0.9999 skewness=0.003525 kurtosis=0.2474 moment_inertia=2.382e+10 radius_gyration= 92.08
203. apix=2.30 min=-4.277 max=4.285 mean=0.001406 sigma=0.9999 skewness=0.002048 kurtosis=0.2567 moment_inertia=2.371e+10 radius_gyration= 92.08
204. apix=2.30 min=-4.256 max=4.277 mean=-0.001445 sigma=0.9999 skewness=-0.001242 kurtosis=0.2521 moment_inertia=2.365e+10 radius_gyration= 92.13
205. apix=2.30 min=-4.279 max=4.239 mean=-0.0009115 sigma=0.9999 skewness=-0.003249 kurtosis=0.2509 moment_inertia=2.361e+10 radius_gyration= 92.02
206. apix=2.30 min=-4.229 max=4.287 mean=0.005883 sigma=0.9999 skewness=0.0003369 kurtosis=0.245 moment_inertia=2.385e+10 radius_gyration= 92.07
207. apix=2.30 min=-4.34 max=4.262 mean=-0.003142 sigma=0.9999 skewness=-0.004288 kurtosis=0.2703 moment_inertia=2.354e+10 radius_gyration= 92.05
208. apix=2.30 min=-4.258 max=4.271 mean=0.008709 sigma=0.9999 skewness=0.002757 kurtosis=0.2606 moment_inertia=2.394e+10 radius_gyration= 92.11
209. apix=2.30 min=-4.284 max=4.25 mean=-0.0009155 sigma=0.9999 skewness=0.002748 kurtosis=0.2544 moment_inertia=2.358e+10 radius_gyration= 91.98
210. apix=2.30 min=-4.311 max=4.265 mean=-0.002893 sigma=0.9999 skewness=0.0003554 kurtosis=0.2687 moment_inertia= 2.35e+10 radius_gyration= 91.96
211. apix=2.30 min=-4.228 max=4.255 mean=0.01277 sigma=0.9999 skewness=0.0007539 kurtosis=0.2543 moment_inertia=2.405e+10 radius_gyration= 92.11
212. apix=2.30 min=-4.254 max=4.295 mean=-0.002443 sigma=0.9999 skewness=0.0003903 kurtosis=0.2642 moment_inertia=2.356e+10 radius_gyration= 92.05
213. apix=2.30 min=-4.206 max=4.293 mean=0.001845 sigma=0.9999 skewness=0.005791 kurtosis=0.2555 moment_inertia=2.367e+10 radius_gyration= 92
214. apix=2.30 min=-4.273 max=4.336 mean=0.003961 sigma=0.9999 skewness=0.001705 kurtosis=0.2626 moment_inertia=2.377e+10 radius_gyration= 92.06
215. apix=2.30 min=-4.244 max=4.28 mean=-0.0007289 sigma=0.9999 skewness=0.005982 kurtosis=0.2522 moment_inertia=2.362e+10 radius_gyration= 92.04
216. apix=2.30 min=-4.249 max=4.283 mean=-0.0006247 sigma=0.9999 skewness=-0.0004979 kurtosis=0.2561 moment_inertia=2.363e+10 radius_gyration= 92.05
217. apix=2.30 min=-4.239 max=4.25 mean=0.0008779 sigma=0.9999 skewness=0.003117 kurtosis=0.2484 moment_inertia= 2.37e+10 radius_gyration= 92.09
218. apix=2.30 min=-4.214 max=4.288 mean=0.005712 sigma=0.9999 skewness=0.002681 kurtosis=0.256 moment_inertia=2.388e+10 radius_gyration= 92.16
219. apix=2.30 min=-4.275 max=4.275 mean=0.003349 sigma=0.9999 skewness=0.0003301 kurtosis=0.2597 moment_inertia=2.374e+10 radius_gyration= 92.04

220 total images
representing 0 particles

Sincerely,

Si Hoon

2022년 1월 12일 (수) 오전 8:14, Ludtke, Steven J. <slu...@bcm.edu>님이 작성:

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