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<p class="MsoNormal"><span style="color:#1F497D">Hi Erhu, <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Thanks you very much this worked like a charm!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Cheers<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Eric<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Comic Sans MS";color:navy">-----------------<o:p></o:p></span></b></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Comic Sans MS";color:navy">Assoc. Prof Eric Hanssen<o:p></o:p></span></b></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Comic Sans MS";color:navy"><o:p> </o:p></span></b></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Comic Sans MS";color:#1F497D">Head - Advanced Microscopy Facility
</span></b><b><span style="font-size:10.0pt;font-family:"Comic Sans MS";color:#1F497D"><o:p></o:p></span></b></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Comic Sans MS";color:#1F497D">Honorary Principal Fellow – Department of Biochemistry and Molecular Biology<o:p></o:p></span></b></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Comic Sans MS";color:#1F497D"><o:p> </o:p></span></b></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Comic Sans MS";color:#1F497D">President Australian Microscopy and Microanalysis Society<o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Comic Sans MS";color:#1F497D"><br>
Bio21 Molecular Science and Biotechnology Institute<br>
</span><span style="font-size:10.0pt;font-family:"Comic Sans MS";color:gray">30 Flemington Road - The University of Melbourne - Victoria 3010 - Australia<br>
email: </span><span style="color:#1F497D"><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">
| Office: +61 3 83442449 | Microscope: +61 3 83442509 <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Comic Sans MS";color:gray">Web:
<a href="http://www.microscopy.unimelb.edu.au/"><span style="color:blue">www.microscopy.unimelb.edu.au</span></a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Comic Sans MS";color:gray"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Comic Sans MS";color:gray"><img border="0" width="245" height="142" id="_x0000_i1028" src="cid:image003.png@01D51222.8C9F3610" alt="bio21">
<img border="0" width="433" height="128" id="_x0000_i1027" src="cid:image004.png@01D51222.8C9F3610" alt="amms-logo"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Erhu Cao [mailto:erhu.cao@biochem.utah.edu]
<br>
<b>Sent:</b> Friday, 24 May 2019 10:23 AM<br>
<b>To:</b> Eric Hanssen; CCPEM@JISCMAIL.AC.UK; 3dem@ncmir.ucsd.edu<br>
<b>Subject:</b> Re: [3dem] order of _rln<o:p></o:p></span></p>
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</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span lang="EN-US">Hi Eric,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">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></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:12.0pt;color:black">From:
</span></b><span lang="EN-US" 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>
</div>
<div>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
</div>
<p class="MsoNormal"><span lang="EN-US">Hi all, <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">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></span></p>
<p class="MsoNormal"><span lang="EN-US">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></span></p>
<p class="MsoNormal"><span lang="EN-US">Eric<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">in: /home/bio21em1/relion/src/exp_model.cpp, line 414<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">in: /home/bio21em1/relion/src/exp_model.cpp, line 414<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">in: /home/bio21em1/relion/src/exp_model.cpp, line 414<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">in: /home/bio21em1/relion/src/exp_model.cpp, line 414<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">in: /home/bio21em1/relion/src/exp_model.cpp, line 414<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">=== Backtrace ===<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/usr/local/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x43c771]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/usr/local/bin/relion_refine_mpi(_ZN10Experiment37divideOriginalParticlesInRandomHalvesEib+0x1c6e) [0x53911e]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/usr/local/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0x3f1) [0x45b861]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/usr/local/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x955) [0x45c725]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/usr/local/bin/relion_refine_mpi(main+0xb2f) [0x42c6ff]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/lib64/libc.so.6(__libc_start_main+0xfd) [0x375be1ed1d]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/usr/local/bin/relion_refine_mpi() [0x42d409]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">==================<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">ERROR: <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">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></span></p>
<p class="MsoNormal"><span lang="EN-US">=== Backtrace ===<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/usr/local/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x43c771]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/usr/local/bin/relion_refine_mpi(_ZN10Experiment37divideOriginalParticlesInRandomHalvesEib+0x1c6e) [0x53911e]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/usr/local/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0x3f1) [0x45b861]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/usr/local/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x955) [0x45c725]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/usr/local/bin/relion_refine_mpi(main+0xb2f) [0x42c6ff]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/lib64/libc.so.6(__libc_start_main+0xfd) [0x375be1ed1d]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/usr/local/bin/relion_refine_mpi() [0x42d409]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">==================<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">ERROR: <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">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></span></p>
<p class="MsoNormal"><span lang="EN-US">=== Backtrace ===<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/usr/local/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x43c771]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/usr/local/bin/relion_refine_mpi(_ZN10Experiment37divideOriginalParticlesInRandomHalvesEib+0x1c6e) [0x53911e]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/usr/local/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0x3f1) [0x45b861]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/usr/local/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x955) [0x45c725]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/usr/local/bin/relion_refine_mpi(main+0xb2f) [0x42c6ff]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/lib64/libc.so.6(__libc_start_main+0xfd) [0x375be1ed1d]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/usr/local/bin/relion_refine_mpi() [0x42d409]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">==================<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">ERROR: <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">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></span></p>
<p class="MsoNormal"><span lang="EN-US">=== Backtrace ===<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/usr/local/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x43c771]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/usr/local/bin/relion_refine_mpi(_ZN10Experiment37divideOriginalParticlesInRandomHalvesEib+0x1c6e) [0x53911e]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/usr/local/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0x3f1) [0x45b861]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/usr/local/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x955) [0x45c725]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/usr/local/bin/relion_refine_mpi(main+0xb2f) [0x42c6ff]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/lib64/libc.so.6(__libc_start_main+0xfd) [0x375be1ed1d]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/usr/local/bin/relion_refine_mpi() [0x42d409]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">==================<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">ERROR: <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">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></span></p>
<p class="MsoNormal"><span lang="EN-US">=== Backtrace ===<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/usr/local/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x43c771]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/usr/local/bin/relion_refine_mpi(_ZN10Experiment37divideOriginalParticlesInRandomHalvesEib+0x1c6e) [0x53911e]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/usr/local/bin/relion_refine_mpi(_ZN14MlOptimiserMpi18initialiseWorkLoadEv+0x3f1) [0x45b861]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/usr/local/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0x955) [0x45c725]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/usr/local/bin/relion_refine_mpi(main+0xb2f) [0x42c6ff]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/lib64/libc.so.6(__libc_start_main+0xfd) [0x375be1ed1d]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/usr/local/bin/relion_refine_mpi() [0x42d409]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">==================<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">ERROR: <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">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></span></p>
<p class="MsoNormal"><span lang="EN-US">[odin:158859] 4 more processes have sent help message help-mpi-api.txt / mpi-abort<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">[odin:158859] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages<o:p></o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Comic Sans MS";color:navy">-----------------</span></b><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Comic Sans MS";color:navy">Assoc. Prof Eric Hanssen</span></b><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Comic Sans MS";color:navy"> </span></b><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Comic Sans MS";color:#1F497D">Head - Advanced Microscopy Facility
</span></b><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Comic Sans MS";color:#1F497D">Honorary Principal Fellow – Department of Biochemistry and Molecular Biology</span></b><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Comic Sans MS";color:#1F497D"> </span></b><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Comic Sans MS";color:#1F497D">President Australian Microscopy and Microanalysis Society</span></b><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Comic Sans MS";color:#1F497D"><br>
Bio21 Molecular Science and Biotechnology Institute<br>
</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Comic Sans MS";color:gray">30 Flemington Road - The University of Melbourne - Victoria 3010 - Australia<br>
email: </span><span lang="EN-US" style="color:#1F497D"><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 lang="EN-US" style="font-size:10.0pt;font-family:"Comic Sans MS";color:gray">
| Office: +61 3 83442449 | Microscope: +61 3 83442509 </span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Comic Sans MS";color:gray">Web:
<a href="http://www.microscopy.unimelb.edu.au/">www.microscopy.unimelb.edu.au</a></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Comic Sans MS";color:gray"> </span><span lang="EN-US"><o:p></o:p></span></p>
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<img border="0" width="433" height="128" id="Picture_x0020_2" src="cid:image006.png@01D51222.8C9F3610" alt="amms-logo"></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <o:p></o:p></span></p>
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