Hi Daniel,

To re-create the coordinate *.star files for each micrograph you can use our script "relion_create_coordinate_files.py". It is available here: https://github.com/OPIC-Oxford/pyrelion-scripts (you will need Scipion software to run it).

This should help you with Relion 1.4 (this might not be needed in 2.0 anymore, I haven't checked recently).

Best wishes,

Juha

On Fri, Feb 10, 2017 at 10:08 PM, Alexander Shkumatov <[log in to unmask]> wrote:

Hi Daniel

you access it as described in RELION manual.

Basically, from a final _data.star you have to re-create coordinate *.star files for each micrograph with, say, *_afterref.star suffix. These files should be in the same dir/ as your micrographs files. Then in "micrograph inspection" of RELION (1.4) you should provide
original "simple" star file with relative path of micrographs and 'afterref' as a "picking rootname" and voila!

I have done it many times in RELION 1.4 but similar principle i believe can be used in RELION2.0

HTH, Alex

> On 10 Feb 2017, at 21:56, Daniel Larsson <[log in to unmask]> wrote:
>
> Hi Alex,
>
> Sure all the info is in the file, but how do one access the particle picking GUI? Do you have a better way instead of my work around?
>
> Regards,
> Daniel
>
>
>> On 10 Feb 2017, at 16:24, Alexander Shkumatov <[log in to unmask]> wrote:
>>
>> Hello Daniel
>> You can parse your _data.star file (without extraction) and create new star files with coordinates for each micrograph. Moreover, you can also include the X/Y shift information (rlnOrigin[X/Y]) or psi angle information from _data.star file to modify the coordinates.
>> Alex
>>
>>> On Feb 10, 2017, at 13:55, Daniel Larsson <[log in to unmask]> wrote:
>>>
>>> To reply to my own question, a college of mine just suggested to make a re-extraction job using the _data.star from the refinement job and then use the Display dialogue for that job to access the picking GUI by choosing the generated coords_suffix_extract.star file. Works just as I wanted.
>>>
>>> Regards,
>>> Daniel
>>
>>
>>
>>
>>>> On 2017-02-10, at 13:39, Daniel Larsson <[log in to unmask]> wrote:
>>>>
>>>> What is the best way if I want to go back to the original micrographs again to manually curate a dataset once I've already extracted the particles. E.g. once I've done 2D classification and pruned my data or even or a 3D refinement, I want to show the coordinates again on the micrographs again and add false negatives or remove false positives. I tried to use the relion_manualpick binary with the flags --i Refine3D/job037/run_data.star and --selection Refine3D/job037/run_data.star, but that did not do what I wanted.
>>>>
>>>> Regards,
>>>> Daniel
>>