 |
 |
Hi Kevin, Did you recompile the mew code after correcting it? Also, perhaps your mask is all-black? Make sure you use the correct threshold for the automasking procedure. HTH, S > Dear Sjor, > > I am currently on the particle polishing step of processing my > protein (~600kDa) and have encounter the same error after multiple > runs. I receive the following error: > > + Reconstructing two halves of shiny particles ... > == Reading input half-reconstructions: > + half1-map: > Refine3D/run04_movie_ct20_data_shiny_half1_class001_unfil.mrc > + half2-map: > Refine3D/run04_movie_ct20_data_shiny_half2_class001_unfil.mrc > == Using a user-provided mask ... > + input mask: Refine3D/postprocess_run04_automask.mrc > == Masking input maps ... > + randomize phases beyond: -247.678 Angstroms > Postprocessing::run ERROR: FSC curve never drops below randomize_fsc_at > > I have looked up and tried a few suggestions from previous post regarding > this error including the additional argument of --bfactor_running_avg 3 > and it did not work. My bfactor.star file includes frames with values and > frames with -nan for BFactorUsedForSharpening and > FittedInterceptGuinierPlot columns. What is the best way to check what is > causing this error or to resolve this issue? My input parameters for > particle polishing includes: Running Average Window: 7 (same value used in > the "Refinement with Movie-Particles" step 8.3 in tutorial), Stddev on > Particle Distance (pix): 300, Highres-limit Per-Frame Maps (A): 6, and > Lowres-limit B-factor Estimation (A): 20. > > Also, I have noticed a few output discrepancy during the Particle > Polishing Step. In my movies, I have 32 frames, but I extracted frames > 3-27 at the "Extraction the Movie-Particles" step. I noticed that the > output files includes frames 1-25; therefore, I was wondering if Relion > always reads the first frame as 1 (if frame 1 is actually frame 3 from the > movie)? If so, then I found it odd that the first frame did not have any > cross-sectional image when displayed it RELION. I saw that there was a bug > in the movie extraction and corrected it as described in known issue > website (http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Known_issue). > > Thank You in Advance, > Kevin > -- Sjors Scheres MRC Laboratory of Molecular Biology Francis Crick Avenue, Cambridge Biomedical Campus Cambridge CB2 0QH, U.K. tel: +44 (0)1223 267061 http://www2.mrc-lmb.cam.ac.uk/groups/scheres