Error for EMAN2 Reference-based boxing in tomograms

[Dong-Hua Chen]

Hi All,

I am trying to use a pdb-converted mrc map (e2pdb2mrc.py xxx.pdb xxx_20A.mrc --center --box 64 --apix 3.436 --res 20) to do Reference-based boxing in my tomograms. I got the following error. Any suggestions? Thanks!

Here is the command for e2spt_tempmatch.py:

e2spt_tempmatch.py tomograms/tomo001_bin4__bin2.hdf  --reference=xxx_20A.mrc --label=xxx --nptcl=500 --dthr=-1.0 --vthr=10.0 --delta=30.0 --sym=c1 --rmedge --rmgold --boxsz=-1 --threads=8

Best regards,

Dong-Hua

E2version.py

EMAN 2.99 ( GITHUB: 2021-12-02 11:37 - commit: 7e92c38 )

Your EMAN2 is running on: Linux-3.10.0-1160.42.2.el7.x86_64-x86_64-with-centos-7.9.2009-Core 3.10.0-1160.42.2.el7.x86_64

Your Python version is: 3.7.12

NOT Writing notes, ppid=-2

Testing 588 orientations...

Locating reference-like particles in tomograms/tomo001_bin4__bin2.hdf (File 1/15)

Will shrink tomogram by 2

Will shrink reference by 4.0

588/588 finished.

removing edge: rotation 98.3

0

Traceback (most recent call last):

  File "/home/eman2-sphire-sparx/bin/e2spt_tempmatch.py", line 260, in <module>

    main()

  File "/home/eman2-sphire-sparx/bin/e2spt_tempmatch.py", line 177, in main

    pkscore/=np.max(pkscore)

  File "<__array_function__ internals>", line 6, in amax

  File "/home/eman2-sphire-sparx/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 2668, in amax

    keepdims=keepdims, initial=initial, where=where)

  File "/home/eman2-sphire-sparx/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 90, in _wrapreduction

    return ufunc.reduce(obj, axis, dtype, out, **passkwargs)

ValueError: zero-size array to reduction operation maximum which has no identity

[Muyuan Chen]

I think it means it is unhappy for finding 0 particles under the criteria. This does not happen often and I did not implement a good error handler. Try reducing vthr to a smaller number (maybe 3) and see if it finds anything? 

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