Thanks :-) Sometimes things are easier than expected.... Best, 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 10:51, Takanori Nakane wrote:
> Hi,
>
>> 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!
>
> Please make symbolic links by absolute paths.
>
> https://www3.mrc-lmb.cam.ac.uk/relion/index.php/FAQs#How_can_I_merge_datasets.2C_potentially_with_different_pixel_sizes.3F
>
>
> e.g.
>
> /absolute_path_to/experiment1/experiment2/Polish/jobXXX ->
> experiment1/Polish/jobXXX
>
> Takanori
>
>> 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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