Re: [scipion-users] relion 3

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

Hi Jonathan,

That's great! Please use the current implementation in my branch while we
are in the process of the new release. We will be very happy to help you
with any problem or take into account your feedback.

The Relion's implementation of motion correction is available in Scipion in
that branch. Within Scipion, you could use it, or motioncor2 or any
global/local alignment method and later combine with the Relion's Bayesian
Polishing, since we take care of the proper generation of the required star
files. In our facility here in Stockholm, we routinely go until 2D
classification and in some cases to initial 3D volume and refinement. Some
of our users also want to take their pre-processed data and go to Relion or
CryoSparc, so I have implemented a couple protocols that are quite useful
for that: "relion - export ctf" and "relion - export particles" .

Regarding the protocols that does not appear...you can always try Ctrl + F
to open the Search Protocol Dialog and check if they appear there. It is
probably due to the old protocols.conf that does not contains the new
protocol. You could remove it and generate again (from the scipion folder):
rm config/protocols.conf
./scipion config

Hope this helps,
Best,
Jose Miguel


On Sat, Feb 23, 2019 at 1:16 AM Jonathan Remis <re...@gm...> wrote:

> Hello Jose Miguel,
>
> We also have interest in using Relion3 from within Scipion.
>
> We currently are trying to use Scipion at our EM facility to monitor data
> as it is collected and typically use Motioncor2 to do the motion
> correction.   Many users want to use Relion3 to do their single particle
> reconstructions but because you are not able to import Motioncor2 fixed
> micrographs into Relion3 they need to re-run motion correction from within
> Relion3.  It would be ideal if we could give them motion corrected
> micrographs that they could directly use in the image processing program of
> their choice.    I was curious if Scipion will or does include access to
> this different multi-core cpu motion correction program?   I don't see it
> in the protocols after following the instructions you have posted in the
> link above.
>
> Thank you for your time-
>
> Jonathan_Remis
>
>
>
>
> On Thu, Feb 21, 2019 at 11:22 AM Jose Miguel de la Rosa Trevin <
> del...@gm...> wrote:
>
>> Hi Daniel,
>>
>> I have updated the protocols in Scipion for support for Relion3. It is
>> beta right now,
>> but it has been used here in Stockholm and also a bit in Madrid. We
>> haven't announced
>> yet because we will wait until the next Scipion release (2.0) for that.
>>
>> I wrote some instructions to use it from the current Scipion version
>> (v1.2.1)
>> https://github.com/delarosatrevin/scipion/wiki/Testing-Relion-3-in-Scipion
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_delarosatrevin_scipion_wiki_Testing-2DRelion-2D3-2Din-2DScipion&d=DwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=D_rs7PhtmkmTUoH64Stdl6OPL5kCXmTvZbb7Ola-aIs&m=WyDyWBGr3WYFt_HcN3ca4g6lI0to6OT4OjaVHX03qM8&s=CRCn6MzQcPw3qmitElhcn8pmM9Kl0tOeUkMbYMZ3j1Y&e=>
>>
>> Please don't hesitate to contact me if you need some help to update the
>> Scipion
>> installation for Relion 3 support.
>>
>> Cheers,
>> Jose Miguel
>>
>>
>> On Thu, Feb 21, 2019 at 8:15 PM Daniel Larsson <dan...@ic...>
>> wrote:
>>
>>> When can we expect to have Relion 3 in Scipion?
>>>
>>> Regards,
>>> Daniel
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
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