Hello everybody,
I would like to ask about a problem when running Gctf local refine. I
have a dataset collected with tilt and I want to estimate the ctf per
particle before extracting the particles and go for 2D classification.
I realised the Gctf --do_local_refine option is not possible inside
RELION, so I am trying to run Gctf out of RELION.
I have a directory with some of my micrographs as a sample and their
correspondent _autopick.star obtained with RELION Autopick.
I run the following commnand:
Gctf-v1.06_sm_30_cu8.0_x86_64 /path/to/micrographs/*.mrc --apix 1.047
--cs 2.7 --kV 300 --ac 0.1 --resL 30 --resH 5 --defL 5000 --defH 50000
--dstep 500 --astm 100 --do_EPA --do_local_refine --boxsuffix
_autopick.star --write_local_ctf --local_overlap 0.80 --local_boxsize
512 --local_radius 1024 --do_validation
also this simpler one: Gctf *.mrc --apix 1.047 --do_EPA
--do_local_refine --boxsuffix _autopick.star
It creates the files _local.ctf and _local.star but they are empty. It
finishes with this error:
Writing out star file micrograph_local.star for local refinement
Using box file micrograph_autopick.star for local refinement
Segmentation fault (core dumped)
Running Gctf without the option --do_local_refine works well.
Thank you in advance for your help,
Adrian
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