RuntimeError: std::exception caused by xform_align_nbest

[lyw8120]

I was trying to do subtomogram averaging, and the command is
e2spt_refine.py sets/template_bin4.lst --reference=sptsgd_03/threed_05.hdf --niter=5 --sym=c1 --mass=3000.0 --goldstandard=30 --pkeep=0.8 --maxtilt=90.0 --threads=10 --ppid=-2

while I got an error

/anaconda3/envs/eman2/bin/e2spt_align.py", line 625, in execute
c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln)
RuntimeError: std::exception

I went the line 625 of e2spt_align.py
I think here is to do alignment work, between ref and b, where ref is the reference 3d image and b is the 3d particle I extracted using the alignment method "rotate_translate_3d_tree" with additional information (aligndic and options.nsoln).
I also search and check the original code in emdata_modular.h/.cpp, and confirm it. I think there is no mistake, but I do not understand what is going on here. could you please tell me an solution? thanks
ps: eman2 was installed from source.
Yaowang

[sludtke42]

The current version of the pipeline uses e2spt_refine_new.py, though the program you ran should still work. Could you run e2iminfo.py sets/template_bin4.lst -as and reply with the first dozen lines or so, as well as e2iminfo.py sptsgd_03/threed_05.hdf -as

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-------------------------------------------------------------------------------------- Steven Ludtke, Ph.D. ***@***.******@***.***>> Baylor College of Medicine Charles C. Bell Jr., Professor of Structural Biology Dept. of Biochemistry Deputy Director, Advanced Technical Cores and Molecular Biology Academic Director, CryoEM Core Co-Director CIBR Center On Aug 26, 2022, at 11:48 PM, Yao-Wang Li ***@***.******@***.***>> wrote: I was trying to do subtomogram averaging, and the command is e2spt_refine.py sets/template_bin4.lst --reference=sptsgd_03/threed_05.hdf --niter=5 --sym=c1 --mass=3000.0 --goldstandard=30 --pkeep=0.8 --maxtilt=90.0 --threads=10 --ppid=-2 while I got an error /anaconda3/envs/eman2/bin/e2spt_align.py", line 625, in execute c=ref.xform_align_nbest("rotate_translate_3d_tree",b, aligndic, options.nsoln) RuntimeError: std::exception I went the line 625 of e2spt_align.py I think here is to do alignment work, between ref and b, where ref is the reference 3d image and b is the 3d particle I extracted using the alignment method "rotate_translate_3d_tree" with additional information (aligndic and options.nsoln). I also search and check the original code in emdata_modular.h/.cpp, and confirm it. I think there is no mistake, but I do not understand what is going on here. could you please tell me an solution? thanks ps: eman2 was installed from source. Yaowang — Reply to this email directly, view it on GitHub<#551>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACPKF2W36STKP2V2QWS2MBTV3GMZVANCNFSM57YV566Q>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>