Re: [scipion-users] relion-autopick protocol

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

Hi Dmitry,

The "optimize" mode is not another protocol, but a mode, i.e, an option
that you should select when filling in the protocol parameter (see attached
image). The relion autopicking should be done in 3 steps:

1) Run the autopick in "optimize" mode for a subset of micrographs (either
selected automatically by the protocol,  covering the defocus range or you
can provide a subset manually created)
2) Open again the protocol after step 1) and click on the wizard to
interactively fine tune the picking parameters (interparticle distance and
threshold). It should open the Xmipp picking interface, but it will launch
the Relion auto-picking program and show the particles.
3) After selecting the good parameters, now you can run the auto-picking
for all the input set of micrographs.

All the 3 steps are done in the same protocol run (box in the processing
tree).

Hope this helps
Best,
Jose Miguel


On Fri, Aug 25, 2017 at 4:52 PM, D.A. Semchonok <sem...@gm...> wrote:

> Dear colleagues,
>
> Does anyone knows how to use relion-autopick protocol?
>
> It asks me to run "optimize" mode first and I have not found that in the
> list of protocols
>
>
> Any suggestions?
>
> Sincerely,
> Dmitry
>
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