Hi, the likely problem is that Relion3 started to add comment line to
the top of _autopick.star file, on which Gctf stumbles.
For us what works is to remove comment line from _autopick.star using
“sed -i -e 1d *_autopick.star” in current directory.
Best
Leonid
Prof. Leonid Sazanov FRS
IST Austria
Am Campus 1
A-3400 Klosterneuburg
Austria
Phone: +43 2243 9000 3026
E-mail: [log in to unmask]
On 17.09.19 11:54, Adrián Plaza Pegueroles wrote:
> 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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