[scipion-users] About particle picking with Xmipp and EMAN2 through Scipion

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

Dear Luigi,

Thanks for providing feedback to us. Regarding your specific issues with
picking, what do you mean by "after providing the references" in Xmipp and
Eman pickers? To the best of my knowledge, both programs generate the
references on-the-fly, after the selection of some particles manually. So,
there is not need to provide pre-computed references such as 2D class
averages.

In the case of EMAN2-Box, both the manual/supervised steps are interwinned
in a very interactive way. On the other hand, in Xmipp3 picker, those steps
are separated in two phases. You first need to picking manually some
micrographs entirely (or a well-defined box in one micrograph is its
contains many particles)...and then switch to "Supervised" mode, where the
algorithm will propose you some particle candidates and you can correct it
(either removing bad proposed particles or adding missing one). The
algorithm will "learn" from that and then in another protocol you can
launch the automatic picking based on that training.

Anyway, if you provide a few micrographs we could try to help about the
parameters selection.

Hope this helps,

Jose Miguel

Scipion Team


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My name is Luigi De Colibus and I’m Post Doc at the Division of Structural
Biology of Oxford University.
I’m writing you because I’m trying to run automated particle picking
programs on my micrographs trough SCIPION.
Surprisingly, despite the fact my virus particle is very big and evident on
the micrographs, neither Xmipp particle picking program nor Boxer in EMAN2
is able to pick correctly the particles after providing the reference.
I guess my settings could be wrong and trying different values has not
helped so far.

It would be great if you could point me in the right direction.
I can send you one of my micrographs if you need to do a test run.

Thanks a lot in advance for your help!

Best Regards

Reply to: luigi at strubi.ox.ac.uk