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Hi, yes, the command from "note.txt" works well. Thanks a lot! Prof. Leonid Sazanov IST Austria Am Campus 1 A-3400 Klosterneuburg Austria Phone: +43 2243 9000 3026 E-mail: [log in to unmask] On 13/08/18 13:24, Takanori Nakane wrote: > Hi, > > OK, the log indicates that multibody refinement itself has finished > successfully. > What happens if you run relion_flex_analyse from the command line? > The command is in the note.txt and should look like: > > `which relion_flex_analyse` --PCA_orient --model > MultiBody/job092/run_model.star --data MultiBody/job092/run_data.star > --bodies bodies.star --o MultiBody/job092/analyse --do_maps --k 5 > >> Also, a combined map of two bodies together is not produced - should it >> be?, or it needs to made separately, e.g. in Chimera? > This is intended. There is no combined map. > > Best regards, > > Takanori Nakane > >> Dear Takanori, >> >> This is the end of "run.out" file: >> >> ?Auto-refine: Refinement has converged, stopping now... >> ?Auto-refine: + Final reconstruction from all particles is saved as: >> MultiBody/job1110/run_ct15_class001.mrc >> ?Auto-refine: + Final model parameters are stored in: >> MultiBody/job1110/run_ct15_model.star >> ?Auto-refine: + Final data parameters are stored in: >> MultiBody/job1110/run_ct15_data.star >> ?Auto-refine: + Final resolution (without masking) is: 3.40645 >> ?Auto-refine: + But you may want to run relion_postprocess to mask the >> unfil.mrc maps and calculate a higher resolution FSC >> >> Last files produced: >> >> run_ct15_half2_body001_unfil.mrc >> run_ct15_half2_body002_unfil.mrc >> run_ct15_half1_body001_unfil.mrc >> run_ct15_half1_body002_unfil.mrc >> run_ct15_data.star >> run_ct15_body001.mrc >> run_ct15_body002.mrc >> run_ct15_body001_angdist.bild >> run_ct15_body002_angdist.bild >> run_ct15_model.star >> run_ct15_sampling.star >> run.out >> >> After that there is no CPU activity, so it does not go into PCA step. >> >> Also, a combined map of two bodies together is not produced - should it >> be?, or it needs to made separately, e.g. in Chimera? >> >> Thanks for your help! >> >> Leonid >> >> Prof. Leonid Sazanov >> IST Austria >> Am Campus 1 >> A-3400 Klosterneuburg >> Austria >> >> Phone: +43 2243 9000 3026 >> E-mail: [log in to unmask] >> >> On 12/08/18 21:08, Takanori Nakane wrote: >>> Hi, >>> >>> Yes, it should work without GPU. >>> >>> A MultiBody job proceeds in two steps. >>> >>> (1) multi-body refinement itself (relion_refine_mpi) >>> (2) PCA analysis (relion_flex_analyser) >>> >>> Could you please look at the log file and see which step failed? >>> Did the first step say "refinement has converged" and produce >>> relevant STAR files? >>> >>> Best regards, >>> >>> Takanori Nakane >>> >>> On 2018/08/12 16:30, Leonid Sazanov wrote: >>>> Hi, great new features in Relion3.0! >>>> >>>> A question - after running multibody refinement we don't get out the >>>> results of PCA analysis, even though this option is set to "yes" in >>>> GUI. The program stops but is not marked as finished. Is it supposed >>>> to be working in CPU version of 3.0beta (the only one we have working >>>> so far)? >>>> >>>> Many thanks! >>>> >>>> ######################################################################## >>>> >>>> To unsubscribe from the CCPEM list, click the following link: >>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1 >>>> >> ######################################################################## >> >> To unsubscribe from the CCPEM list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1 >> > ######################################################################## To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1