Hi Bjoern,
thank you! I was worried to screw up something because of the other
referrals in this file, but changing only the reference to the
micrographs directory (and some other things I had overlooked) it seems
to run smoothly now!
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]
------------------------------------------------------------------------
Am 19.06.2017 um 10:13 schrieb Bjoern Forsberg:
> 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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