Hi,
Hmm, it seems that the code got mixed up when I back-ported some
commits into 3.0. Since we will start the beta testing of 3.1
in near future (don't ask me the exact date; I myself don't know),
I will leave 3.0 as it is now.
Best regards,
Takanori Nakane
> Hi Takanori
>
> This was in 3.0.7. The printout when relion_preprocess is fired says it
> should be use_ctf_in_mic. But the effect only takes place with keep ctfs
> as
> you mentioned.
>
> Best wishes
>
>
> On Wed, 11 Sep 2019, 11:43 Takanori Nakane, <[log in to unmask]>
> wrote:
>
>> 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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>> >
>>
>>
>>
>
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