Hi,
I have a related question: Stupidly, I made a subdirectory within
the directory structure in one relion-3.1 project (where all
subdirectories Import, Class3D, etc. are) and did a whole run with
particles different from the ones used in the main directory and picked
separately from the same micrographs. Is there an easy way to combine
these particles?
In other words, I'd like to combine
experiment1/Refine3D/jobxxx/run_data.star with
experiment1/experiment2/Refine3D/jobyyy/run_data.star. I am not sure
whether I could use absolute paths for this!
Thanks, Dieter
------------------------------------------------------------------------
Dieter Blaas,
Max 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,
Mobile: 0043 699 1942 1659
e-mail: [log in to unmask]
------------------------------------------------------------------------
On 10.11.2020 10:12, Takanori Nakane wrote:
> Hi,
>
> As explained in the wiki, particles can be joined and refined together
> before Polish. When you polish it, supply run_data.star that contains
> particles from both datasets, but give a motion correction STAR file that
> contains only one dataset. This Polish job will output particles
> only from the dataset. Then run another Polish job with a motion
> correction
> STAR file that contains the other dataset. Then join two shiny.star.
>
> Best regards,
>
> Takanori Nakane
>
> On 2020/11/10 9:09, Ahmad Khalifa wrote:
>> Our recommendation is to assign different optics groups to each
>> dataset and
>> Polish separately. See
>> https://www3.mrc-lmb.cam.ac.uk/relion/index.php/Pixel_size_issues#How_can_I_merge_datasets_with_different_pixel_sizes.3F
>> <https://www3.mrc-lmb.cam.ac.uk/relion/index.php/Pixel_size_issues#How_can_I_merge_datasets_with_different_pixel_sizes.3F>.
>>
>>
>> Hi Takanori, just to confirm, when I assign two optics groups, the
>> two datasets wll be polished separately, is that correct? Or do you
>> mean polish separately and only after the polishing, join the datasets?!
>>
>> Cheers.
>>
>> On Mon, Nov 9, 2020 at 11:26 PM Takanori Nakane
>> <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>>
>> Hi,
>>
>> Which did you join, particle STAR files or motion correction STAR
>> files?
>>
>> You can give a joined motion correction STAR file to polish all
>> particles
>> from both datasets in one go, but I don't recommend this.
>>
>> I don't trust "identical settings". I sometimes see dose,
>> magnification, etc
>> to be slightly different between datasets.
>>
>> Our recommendation is to assign different optics groups to each
>> dataset and
>> Polish separately. See
>> https://www3.mrc-lmb.cam.ac.uk/relion/index.php/Pixel_size_issues#How_can_I_merge_datasets_with_different_pixel_sizes.3F
>> <https://www3.mrc-lmb.cam.ac.uk/relion/index.php/Pixel_size_issues#How_can_I_merge_datasets_with_different_pixel_sizes.3F>.
>>
>> Best regards,
>>
>> Takanori Nakane
>>
>> On 2020/11/10 7:16, Dylan Noone wrote:
>> > Hey all,
>> >
>> > I was wondering what to do if you have 2 data collections,
>> with identical settings e.g. ang.pix, and you have joined them using
>> the join star
>> function
>> > and want to subsequently do polishing on refined particles
>> from both these sets.
>> >
>> > For instance, for the micrographs input, where it says (from
>> motioncorr) can I simply put the joined star file, or do I need to
>> somehow split
>> the data
>> > again?
>> >
>> > Cheers,
>> > Dylan Noone
>> >
>> >
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