Hi Everyone,

I am trying to perform particle polishing in Relion v2.1.b1

I have motion-corrected my raw frames into average DW.mrc files without saving the aligned movie frames. I then refined a structure using only the DW.mrc files. 

Realizing that I need the original aligned movie frames to perform particle polishing, I re-ran motioncor2 using the same parameters and then followed the instructions of the Relion2.1 tutorial: I renamed the movie files so that mic001_DW.mrc goes to mic001_DW_movie.mrcs, placed them in the same directory as the DW.mrc files, and imported them into relion using the Import tab. 

I then ran the following command to extract the particles form the movies:

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relion_preprocess --i ./Import/job004/movies.star --reextract_data_star run_it017_data.star --part_dir MovieRefine/job010/ --list_star MovieRefine/job010/micrographs_movie_list.star --join_nr_mics 50 --extract --extract_movies --extract_size 400 --movie_name movie --first_movie_frame 1 --last_movie_frame 48 --avg_movie_frames 1 --norm --bg_radius 150 --white_dust -1 --black_dust -1 --invert_contrast
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where “run_it017_data.star” is the data.star file from the last iteration of a 3D auto-refinement job.

Unfortunately, no particles are extracted and it only spits out warnings like this for each micrograph:

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WARNING: no particles on micrograph: ../new_data/Leginon/17may25c/rawdata/17may25c_c_00010gr_00022sq_v02_00002hln_00005enn-a-DW_movie.mrcs
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(I checked the path and the micrograph indeed exists)

I manually checked the coordinates of the first few particles in “run_it017_data.star” in the old DW.mrc files, the new DW.mrc files (from the new motioncor2 job), and the average of the movie.mrc files (averaged using relion_image_handler). The particles were all in the right place. I was even able to do an extraction of the particles on the “run_it017_data.star” from the new DW.mrc files. So I am confident that the new aligned movies files are good. 

I think the problem might lie in the recognition of the new movie files. Does anyone have any ideas on this? 

I would like to directly submit a .box or .star coordinate file to extract the movies, but if try I use the “--coord_suffix” flag, Relion spits out the error:

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ERROR: 
Preprocessing::initialise ERROR: when extracting movies, you have to provide a --reextract_data_star file.
 
File: /scratchLocal/2.1.b1/relion/src/preprocessing.cpp line: 148
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Does anyone know a way around this so that I can directly submit the movies for extraction?

Thank you very much for your time and expertise!!

Ambrose Plante
Weill Cornell Medical College