Re: [scipion-users] xmipp3 - reconstruct significant script. Export data from xmipp to scipion

[Grigory S. <sha...@gm...>]

Hi,

I believe this is a bug. It should be possible to import particles from
Xmipp/Reion/Frealign program and get both particles set and classes set. It
works, for example, for relion particle star files (after classification),
however the model.star has to be present in the same import folder.
As for the import from xmipp, if you import images.xmd after CL2D, you get
both outputParticles and outputClasses, however the representatives for
these classes are Null. This is the problem.

Dmitry, I believe the current solution for you is to re-run xmipp cl2d
within scipion and then proceed with signficant protocol.

Best regards,
Grigory

--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
Institute of Genetics and Molecular and Cellular Biology
Integrated Structural Biology Department (CBI)
1, rue Laurent Fries
67404 Illkirch, France
tel. 03 69 48 51 00
e-mail: sh...@ig...

On Tue, Nov 1, 2016 at 7:32 PM, Carlos Oscar Sorzano <co...@cn...>
wrote:

> Dear Dmitry,
>
> I'm not sure I get your question. If you work inside Scipion, calling
> reconstruct_significant should be transparent (it accepts a set of classes
> or a set of averages). Internally, it constructs a metadata that is passed
> to Xmipp. If you are coming from outside Scipion, I think you cannot create
> a set of averages or classes directly from import, but I may be wrong.
>
> Kind regards, Carlos Oscar
>
> On 11/01/16 16:17, Dmitry Semchonok wrote:
>
> Dear colleagues,
>
> I would like to run the *xmipp3 - reconstruct significant *script in
> SCIPION.
>
> I run 2D classification in xmipp.
>
> I imported images (class results) after 2D classification (*.mrcs format)
> to the SCIPION.
>
> But after importing these images - (class results) the SCIPION either
> 1. can not see them
> 2. if you export *.mrcs file with *.xml - doesn't want to run the *xmipp3
> - reconstruct significant* script
>
> Protocol failed: Unrecognized type to create MDObject
>
>
> Could you prompt - *what* and* how* I can export from xmipp to SCIPION
> that I could run *xmipp3 - reconstruct significant *script
>
>
> Thank you.
>
> Sincerely,
> Dmitry
>
>
>
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> Carlos Oscar Sánchez Sorzano                  e-mail:   co...@cn...
> Biocomputing unit                             http://biocomp.cnb.csic.es
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