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<p class="MsoNormal">Hi Eric,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">This issue also occurred to me, and I was able to solve this issue by deleting the column “_rlnRandomSubset #19” carried over from cryosparc.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">3dem <3dem-bounces@ncmir.ucsd.edu> on behalf of Eric Hanssen <ehanssen@unimelb.edu.au><br>
<b>Date: </b>Thursday, May 23, 2019 at 6:01 PM<br>
<b>To: </b>"CCPEM@JISCMAIL.AC.UK" <CCPEM@JISCMAIL.AC.UK>, "3dem@ncmir.ucsd.edu" <3dem@ncmir.ucsd.edu><br>
<b>Subject: </b>[3dem] order of _rln<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi all, <o:p></o:p></p>
<p class="MsoNormal">After doing a couple of 2d and 3D steps in cryosparc I have imported particles positions back in relion, re-extracted them, run 2D classes, 3D classes, create an initial model. However when I run the 3D refinement it crashes straight away.
see error below. <o:p></o:p></p>
<p class="MsoNormal">Is the order of the _rln field important? Since that is the only thing I can see different in the particle.star.
<o:p></o:p></p>
<p class="MsoNormal">Eric<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">in: /home/bio21em1/relion/src/exp_model.cpp, line 414<o:p></o:p></p>
<p class="MsoNormal">in: /home/bio21em1/relion/src/exp_model.cpp, line 414<o:p></o:p></p>
<p class="MsoNormal">in: /home/bio21em1/relion/src/exp_model.cpp, line 414<o:p></o:p></p>
<p class="MsoNormal">in: /home/bio21em1/relion/src/exp_model.cpp, line 414<o:p></o:p></p>
<p class="MsoNormal">in: /home/bio21em1/relion/src/exp_model.cpp, line 414<o:p></o:p></p>
<p class="MsoNormal">=== Backtrace ===<o:p></o:p></p>
<p class="MsoNormal">/usr/local/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x43c771]<o:p></o:p></p>
<p class="MsoNormal">/usr/local/bin/relion_refine_mpi(_ZN10Experiment37divideOriginalParticlesInRandomHalvesEib+0x1c6e) [0x53911e]<o:p></o:p></p>
<p class="MsoNormal">/usr/local/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0x3f1) [0x45b861]<o:p></o:p></p>
<p class="MsoNormal">/usr/local/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x955) [0x45c725]<o:p></o:p></p>
<p class="MsoNormal">/usr/local/bin/relion_refine_mpi(main+0xb2f) [0x42c6ff]<o:p></o:p></p>
<p class="MsoNormal">/lib64/libc.so.6(__libc_start_main+0xfd) [0x375be1ed1d]<o:p></o:p></p>
<p class="MsoNormal">/usr/local/bin/relion_refine_mpi() [0x42d409]<o:p></o:p></p>
<p class="MsoNormal">==================<o:p></o:p></p>
<p class="MsoNormal">ERROR: <o:p></o:p></p>
<p class="MsoNormal">ERROR: one of your half sets has no segments. Helical half-sets are always per-filament. Provide at least 2 filaments.<o:p></o:p></p>
<p class="MsoNormal">=== Backtrace ===<o:p></o:p></p>
<p class="MsoNormal">/usr/local/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x43c771]<o:p></o:p></p>
<p class="MsoNormal">/usr/local/bin/relion_refine_mpi(_ZN10Experiment37divideOriginalParticlesInRandomHalvesEib+0x1c6e) [0x53911e]<o:p></o:p></p>
<p class="MsoNormal">/usr/local/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0x3f1) [0x45b861]<o:p></o:p></p>
<p class="MsoNormal">/usr/local/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x955) [0x45c725]<o:p></o:p></p>
<p class="MsoNormal">/usr/local/bin/relion_refine_mpi(main+0xb2f) [0x42c6ff]<o:p></o:p></p>
<p class="MsoNormal">/lib64/libc.so.6(__libc_start_main+0xfd) [0x375be1ed1d]<o:p></o:p></p>
<p class="MsoNormal">/usr/local/bin/relion_refine_mpi() [0x42d409]<o:p></o:p></p>
<p class="MsoNormal">==================<o:p></o:p></p>
<p class="MsoNormal">ERROR: <o:p></o:p></p>
<p class="MsoNormal">ERROR: one of your half sets has no segments. Helical half-sets are always per-filament. Provide at least 2 filaments.<o:p></o:p></p>
<p class="MsoNormal">=== Backtrace ===<o:p></o:p></p>
<p class="MsoNormal">/usr/local/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x43c771]<o:p></o:p></p>
<p class="MsoNormal">/usr/local/bin/relion_refine_mpi(_ZN10Experiment37divideOriginalParticlesInRandomHalvesEib+0x1c6e) [0x53911e]<o:p></o:p></p>
<p class="MsoNormal">/usr/local/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0x3f1) [0x45b861]<o:p></o:p></p>
<p class="MsoNormal">/usr/local/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x955) [0x45c725]<o:p></o:p></p>
<p class="MsoNormal">/usr/local/bin/relion_refine_mpi(main+0xb2f) [0x42c6ff]<o:p></o:p></p>
<p class="MsoNormal">/lib64/libc.so.6(__libc_start_main+0xfd) [0x375be1ed1d]<o:p></o:p></p>
<p class="MsoNormal">/usr/local/bin/relion_refine_mpi() [0x42d409]<o:p></o:p></p>
<p class="MsoNormal">==================<o:p></o:p></p>
<p class="MsoNormal">ERROR: <o:p></o:p></p>
<p class="MsoNormal">ERROR: one of your half sets has no segments. Helical half-sets are always per-filament. Provide at least 2 filaments.<o:p></o:p></p>
<p class="MsoNormal">=== Backtrace ===<o:p></o:p></p>
<p class="MsoNormal">/usr/local/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x43c771]<o:p></o:p></p>
<p class="MsoNormal">/usr/local/bin/relion_refine_mpi(_ZN10Experiment37divideOriginalParticlesInRandomHalvesEib+0x1c6e) [0x53911e]<o:p></o:p></p>
<p class="MsoNormal">/usr/local/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0x3f1) [0x45b861]<o:p></o:p></p>
<p class="MsoNormal">/usr/local/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x955) [0x45c725]<o:p></o:p></p>
<p class="MsoNormal">/usr/local/bin/relion_refine_mpi(main+0xb2f) [0x42c6ff]<o:p></o:p></p>
<p class="MsoNormal">/lib64/libc.so.6(__libc_start_main+0xfd) [0x375be1ed1d]<o:p></o:p></p>
<p class="MsoNormal">/usr/local/bin/relion_refine_mpi() [0x42d409]<o:p></o:p></p>
<p class="MsoNormal">==================<o:p></o:p></p>
<p class="MsoNormal">ERROR: <o:p></o:p></p>
<p class="MsoNormal">ERROR: one of your half sets has no segments. Helical half-sets are always per-filament. Provide at least 2 filaments.<o:p></o:p></p>
<p class="MsoNormal">=== Backtrace ===<o:p></o:p></p>
<p class="MsoNormal">/usr/local/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x43c771]<o:p></o:p></p>
<p class="MsoNormal">/usr/local/bin/relion_refine_mpi(_ZN10Experiment37divideOriginalParticlesInRandomHalvesEib+0x1c6e) [0x53911e]<o:p></o:p></p>
<p class="MsoNormal">/usr/local/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0x3f1) [0x45b861]<o:p></o:p></p>
<p class="MsoNormal">/usr/local/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x955) [0x45c725]<o:p></o:p></p>
<p class="MsoNormal">/usr/local/bin/relion_refine_mpi(main+0xb2f) [0x42c6ff]<o:p></o:p></p>
<p class="MsoNormal">/lib64/libc.so.6(__libc_start_main+0xfd) [0x375be1ed1d]<o:p></o:p></p>
<p class="MsoNormal">/usr/local/bin/relion_refine_mpi() [0x42d409]<o:p></o:p></p>
<p class="MsoNormal">==================<o:p></o:p></p>
<p class="MsoNormal">ERROR: <o:p></o:p></p>
<p class="MsoNormal">ERROR: one of your half sets has no segments. Helical half-sets are always per-filament. Provide at least 2 filaments.<o:p></o:p></p>
<p class="MsoNormal">[odin:158859] 4 more processes have sent help message help-mpi-api.txt / mpi-abort<o:p></o:p></p>
<p class="MsoNormal">[odin:158859] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages<o:p></o:p></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Comic Sans MS";color:navy;mso-fareast-language:EN-AU">-----------------</span></b><o:p></o:p></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Comic Sans MS";color:navy;mso-fareast-language:EN-AU">Assoc. Prof Eric Hanssen</span></b><o:p></o:p></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Comic Sans MS";color:navy;mso-fareast-language:EN-AU"> </span></b><o:p></o:p></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Comic Sans MS";color:#1F497D;mso-fareast-language:EN-AU">Head - Advanced Microscopy Facility
</span></b><o:p></o:p></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Comic Sans MS";color:#1F497D;mso-fareast-language:EN-AU">Honorary Principal Fellow – Department of Biochemistry and Molecular Biology</span></b><o:p></o:p></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Comic Sans MS";color:#1F497D;mso-fareast-language:EN-AU"> </span></b><o:p></o:p></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Comic Sans MS";color:#1F497D;mso-fareast-language:EN-AU">President Australian Microscopy and Microanalysis Society</span></b><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Comic Sans MS";color:#1F497D;mso-fareast-language:EN-AU"><br>
Bio21 Molecular Science and Biotechnology Institute<br>
</span><span style="font-size:10.0pt;font-family:"Comic Sans MS";color:gray;mso-fareast-language:EN-AU">30 Flemington Road - The University of Melbourne - Victoria 3010 - Australia<br>
email: </span><span style="color:#1F497D;mso-fareast-language:EN-AU"><a href="mailto:ehanssen@unimelb.edu.au"><span style="font-size:10.0pt;font-family:"Comic Sans MS";color:gray">ehanssen@unimelb.edu.au</span></a></span><span style="font-size:10.0pt;font-family:"Comic Sans MS";color:gray;mso-fareast-language:EN-AU">
| Office: +61 3 83442449 | Microscope: +61 3 83442509 </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Comic Sans MS";color:gray;mso-fareast-language:EN-AU">Web:
<a href="http://www.microscopy.unimelb.edu.au/">www.microscopy.unimelb.edu.au</a></span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Comic Sans MS";color:gray;mso-fareast-language:EN-AU"> </span><o:p></o:p></p>
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<img border="0" width="433" height="128" style="width:4.5104in;height:1.3333in" id="Picture_x0020_2" src="cid:image002.png@01D51194.9CA88720" alt="amms-logo"></span><o:p></o:p></p>
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