Hi,
Which version are you talking about?
For 3.0, it is --use_ctf_in_mic.
In 3.1, it will be --keep_ctfs_micrographs.
Best regards,
Takanori Nakane
> Okay sorry for not doing it first, but I dug through the source and found
> that the correct option was --keep_ctfs_micrographs in contrast to the
> command printout.
>
> Best wishes
> Shintaro
>
> On Wed, Sep 11, 2019 at 11:10 AM Shintaro Aibara
> <[log in to unmask]>
> wrote:
>
>> Dear Relion Team :)
>>
>> I was just trying to run an extraction job with --use_ctf_in_mic,
>> (Either
>> blank, 1, true) , but relion still seems to pull the defocus information
>> from my join_particles.star. At least it appears this way since the
>> _extract.star it is producing seems to have the incorrect values.
>>
>> Am I missing something here? any input will be greatly appreciated.
>>
>> Best wishes
>> Shintaro
>>
>> version 3.0.7
>> command:
>>
>> `which relion_preprocess_mpi` --i CtfFind/job396/micrographs_ctf.star
>> --reextract_data_star JoinStar/job386/join_particles.star --recenter
>> --recenter_x 0 --recenter_y 0 --recenter_z 0 --part_star
>> Extract/job471/particles.star --part_dir Extract/job471/ --extract
>> --extract_size 450 --norm --bg_radius 168 --white_dust -1 --black_dust
>> -1
>> --invert_contrast --use_ctf_in_mic
>> echo CtfFind/job396/micrographs_ctf.star >
>> Extract/job471/coords_suffix_extract.star
>>
>
>
> --
> Yours Sincerely,
> Shintaro Aibara
>
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