Re: [scipion-users] Combining 2 dataset --- coordinates/extraction issue

[Pablo C. <pc...@cn...>]

Please, if someone is interested in this follow this thread at github 
issues:

https://github.com/I2PC/scipion/issues/2066


On 9/11/19 13:41, Juha Huiskonen wrote:
> Dear All,
>
> I am having the same issue.  I have data collected in two different 
> sessions and they have been exported from two different raw data 
> folders. When I combine two SetOfParticels using 'scipion - join sets' 
> and try to run 'relion - 3D auto-refine' I get the following error:
>
> 00029:     File 
> "/projappl/project_2001566/apps/scipion/2.0/software/lib/python2.7/site-packages/relion/convert/convert.py", 
> line 757, in convertBinaryFiles
> 00030:       pw.utils.createLink(rootDir, outputRoot)
> 00031:     File 
> "/projappl/project_2001566/apps/scipion/2.0/pyworkflow/utils/path.py", 
> line 250, in createLink
> 00032:       relsource = join(relpath(sourcedir, destdir), 
> basename(source))
> 00033:     File 
> "/projappl/project_2001566/apps/scipion/2.0/software/lib/python2.7/posixpath.py", 
> line 428, in relpath
> 00034:       raise ValueError("no path specified")
> 00035:   ValueError: no path specified
> 00036:   Protocol failed: no path specified
> 00037:   FAILED: convertInputStep, step 1
>
> Best wishes,
> Juha
>
> On Thu, Nov 7, 2019 at 6:07 PM Dmitry Semchonok <Sem...@gm... 
> <mailto:Sem...@gm...>> wrote:
>
>     Dear colleagues,
>
>     I have 2 sets of particles from different micrographs that have
>     the same pixel size.
>
>     I want to join (combine) them and run all together.
>
>     What can be the strategy to do that?
>
>
>     What I did
>
>     a)Combined 2 sets of micrographs (with which I worked independently).
>
>     Combined 2 sets of particles;
>
>     Tried to extract the combo coordinates from the combined micrographs.
>
>     Error --- part of them extracted; part of them has wrong coordinates.
>
>     And even with wrong coordinates if I run the 3d auto refinement I
>     get the error Protocol failed: no path specified.
>
>     b)Combined all the micrographs in 1 project.
>
>     Run MotionCor + CTF estimation
>
>     Somehow import the combined coordinates from a) to this new project.
>
>     Re-extract the coordinates.
>
>     So I have a questions:
>
>     -Why a) doesn’t work? Is there a bug?
>
>     -How to export/import the combined coordinates into the new project?
>
>     Amy other suggestions?
>
>     p.s. when/if I succeed with a) with the particle polishing and ctf
>     refinement work? The 2 datasets have different dose rate info.
>
>     Thank you!
>
>     Sincerely,
>
>     Dmitry
>
>     _______________________________________________
>     scipion-users mailing list
>     sci...@li...
>     <mailto:sci...@li...>
>     https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*