sludtke42
commented
1 year ago 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
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 GitHubhttps://github.com/cryoem/eman2/issues/551, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACPKF2W36STKP2V2QWS2MBTV3GMZVANCNFSM57YV566Q. You are receiving this because you are subscribed to this thread.Message ID: @.***>
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