Hello Kevin,

What works for me is extracting the particles in RELION from a  
micrographs_ctf.star obtained inside RELION containing defocus values  
per micrograph. Once you have the particles.star you can replace the  
columns rlnDefocusU, rlnDefocusV, and also rlnDefocusAngle with the  
per particle calculated values in your _local.star files. If you wish  
I can send you a script to do so.

Best,
Adrian

Quoting Kevin Martin <[log in to unmask]>:

> Dear all,
>
> i'm facing some problems while attempting to extract particles from  
> a tilted collection after local ctf estimation.
> Here is what i've done.
>
> I created a folder on the root of my relion pipeline directory named "GCTF"
> Inside this directory, i linked my .mrc files and their  
> corresponding coordinates _autopick.star.
>
> I ran gctf per-particle local estimation from the shell using this command :
>
> /opt/Gctf_v1.18_b2/Gctf_v1.18_b2_sm61_cu8.0  
> in24981-8/raw/Images-Disc1/GridSquare_5312228/Data/*.mrc --do_EPA 1  
> --apix 0.83 --kV 300 --Cs 2.7 --do_local_refine 1 --do_validation 1  
> --boxsuffix _autopick.star
>
> This is an example but in fact i have to launch this command many  
> time since i have multiple "GridSquare_531XXX folder. I just wanted  
> to follow the path i used when i import my movies at the beginning.
>
> Anyway, it works well and i created .ctf ; .epa ; _EPA.log ;  
> _gctf.log ; _local.star and .pow files.
> A file named micrographs_all_gctf.star was also created in the first folder.
>
> Then i import my _local.star coordinate inside Relion 3.1.
> The main problem occurs during the extraction job.
>
> I use as input the corrected_micrographs.star generated by  
> MotionCorr (containing .mrc files i linked for the local ctf  
> estimation), and i input the coordinate _local.star.
>
> The first error is that relion can't find the coordinate (see below)
>
> Warning: coordinate file  
> Import/job110/in24981-8/raw/Images-Disc1/GridSquare_5312561/Data/FoilHole_5353091_Data_5320469_5320471_20200208_100409_fractions_local.star does not  
> exist..
>
> When i go through the Import/job110 directory, i can see the  
> following path :  
> GCTF/in24981-8/raw/Images-Disc1/GridSquare_XXX/Data/XXX_local.star.
>
> My idea was to remove the "GCTF" directory in order to keep the  
> following path :  
> in24981-8/raw/Images-Disc1/GridSquare_XXX/Data/XXX_local.star in  
> order to help relion to find the correct path, where my _local.star  
> files are.
>
> But when i want to relaunch the extraction job this error occurs :
>
> in: /home/install/code/relion-3.1/src/jaz/obs_model.cpp, line 730
> ERROR:
>
> === Backtrace  ===
> /cm/shared/apps/relion-3.1-b/bin/relion_preprocess(_ZN11RelionErrorC1ERKSsS1_l+0x41)  
> [0x43d741]
> /cm/shared/apps/relion-3.1-b/bin/relion_preprocess(_ZNK16ObservationModel14getOpticsGroupERK13MetaDataTablel+0xef)  
> [0x47301f]
> /cm/shared/apps/relion-3.1-b/bin/relion_preprocess(_ZN13Preprocessing33extractParticlesFromOneMicrographER13MetaDataTable8FileNameiS2_S2_RllRdS4_S4_S4_+0x2c58)  
> [0x44a458]
> /cm/shared/apps/relion-3.1-b/bin/relion_preprocess(_ZN13Preprocessing31extractParticlesFromFieldOfViewE8FileNamel+0x5c3)  
> [0x44d353]
> /cm/shared/apps/relion-3.1-b/bin/relion_preprocess(_ZN13Preprocessing19runExtractParticlesEv+0x2e6)  
> [0x44de76]
> /cm/shared/apps/relion-3.1-b/bin/relion_preprocess(_ZN13Preprocessing3runEv+0x12)  
> [0x44e0f2]
> /cm/shared/apps/relion-3.1-b/bin/relion_preprocess(main+0x3d) [0x41c48d]
> /lib64/libc.so.6(__libc_start_main+0xf5) [0x2aaab74fb3d5]
> /cm/shared/apps/relion-3.1-b/bin/relion_preprocess() [0x41cd1f]
> ==================
> ERROR:
>
> By the way, i tried so many combinaison, and it systematically  
> return a relion's problem, even if i import the  
> micrographs_all_gctf.star.
> Any help will be appreciated because i'm stuck through this problem...
>
> Best regards
>
> --
> KEVIN MARTIN
>
> PharmD-PhD student
> Centre de biochimie structurale (CBS)
> 29, Rue de Navacelles
> FR-34090 Montpellier
> [log in to unmask]
>
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-- 
Adrián Plaza Pegueroles
Phd student
Center for Biological Research Margarita Salas (CSIC)
Ramiro de Maeztu, 9.
28040. Madrid. Spain
[log in to unmask]
+34 91 837 31 12 ext 4368

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