Re: [scipion-users] Particle Images from ml2d

[Jose M. de la R. T. <del...@gm...>]

Hi Jonathan,

In Scipion the output of any 2D classification method should generate a
SetOfClasses2D as output. Independently of the package used (EMAN, Xmipp,
Relion, Spider, etc). You should be able to open classes and the particles
associated to each classes. In the 2D case, these particles should contain
the 2D alignment.

Could you provide more details about your specific problem? (in order to
detect if the is some bug over there).
First, what version of Scipion are you using? Second, if you browse in the
ML2D run folder, and go to the extra, can you find the generated .xmd files
for each iteration? They looks like having the correct alignment parameters
in Xmipp? (MDL_SHIFTX, etc)

We are happy to help to overcome this issue and continue with your
processing.

Bests,
Jose Miguel.


On Wed, Aug 24, 2016 at 12:39 PM, List, Jonathan <jon...@ph...>
wrote:

> Hi
>
> we are currently using scipion for generating class averages of DNA
> origami structures. We optained best result with the xmipp ml2d algorithm.
> Sadly we were not able to access the single particles for the classes in
> the aligned state  (it worked for other algorithms). The "aply
> gemometry" checkbox charged something but did not result in the correct
> alignmet like in the class average image. Also clicking on
> summary/ouput/classes insted of "analyse results" which sometimes did the
> trick for the old xmipp did not work. Do you know a way to generate this
> correctly aligned particle stack from ml2d runs?
>
> Greetings and thanks
>
> Jonathan List
>
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