Hi Dieter,
1) Re-extraction of a data.star will go to the referenced micrographs.
If you want to re-extract from new micrographs, the easiest solution is
likely to make a copy of the data.star-file, and replace the micrograph
prefix/suffix by a new one matching the new motioncor-data, using
search-replace, sed, or something of the sort.
2) I noticed this as well, and it will be fixed. The intended behavior
is to return all available flags when a command is run either with no
flags, with -h, or --help.
/Björn
On 06/19/2017 07:10 AM, Dieter Blaas wrote:
> Dear Sjors and all,
>
> I have 2 questions:
>
> 1) I did a reconstruction by using movie frames 4 to 20. I now want to
> see if I get to a better resolution by using e.g. frames 3 to 17:
>
> I did run the corresponding motioncor2 followed by Ctfrun (don't know
> whether this is necessary or the values will largely remain the same).
> What is the best way to extract these new particle images by using the
> old run_data.star file from the refinement run on frames 4 - 20? In
> this file I see references to the previous extraction job and to the
> micrographs. What do I need to change?
>
> 2) It appears to me that "relion_mask_create" has changed in
> relion-2.1 beta 0: calling it from command line gives:
>
> ERROR:
> Either provide --i to apply a mask, OR --create_from to create a new mask
> File: /opt/relion/src/apps/mask_create.cpp line: 66
>
> and "relion_mask_create --create_from" gives:
>
> ERROR:
> Either provide --i to apply a mask, OR --create_from to create a new mask
> File: /opt/relion/src/apps/mask_create.cpp line: 66
>
> instead of listing the parameters. Is this the intended behavior?
>
> Thanks a lot for hints, Dieter
>
> ------------------------------------------------------------------------
> Dieter Blaas,
> Max F. Perutz Laboratories
> Medical University of Vienna,
> Inst. Med. Biochem., Vienna Biocenter (VBC),
> Dr. Bohr Gasse 9/3,
> A-1030 Vienna, Austria,
> Tel: 0043 1 4277 61630,
> Fax: 0043 1 4277 9616,
> e-mail: [log in to unmask]
> ------------------------------------------------------------------------
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