Hi Daniel,
Thanks a lot. It would be nice to try scripts.
Best,
Sergey
2018-06-01 10:37 GMT+02:00 Daniel Castano Diez <[log in to unmask]>:
> Hi Sergey,
>
>
> please note that the interconversion tools between Dynamo and Relion for
> STA have not yet been included/documented in the release that you can
> currently download in our page, but we do have some scripts for that task.
> Drop me a mail if you want to try them.
>
> cheers,
> D.
> --
> Daniel Castaño-Díez
> www.dynamo-em.org
> +41(0) 6138 73214
> Bio-EM Lab at C-CINA
> Biozentrum, University of Basel
>
>
>
>
>
> On 01 Jun 2018, at 10:23, Sergey Nazarov <[log in to unmask]> wrote:
>
> Hi Sjors,
> Sure, thanks a lot.
> Best,
> Sergey
>
> 2018-06-01 10:22 GMT+02:00 Sjors Scheres <[log in to unmask]>:
>
>> Hi Sergey,
>> I am afraid this has not been high on the list, and will not make it into
>> 3.0. Perhaps using dynamo as Alister suggests would be easiest.
>> Best,
>> Sjors
>>
>> > Hi Sergey,
>> >
>> > Not sure if this has been implemented in relion, but it's easy to do in
>> > dynamo!
>> >
>> > I've jotted down some example code below, dynamo also has tools for
>> > converting the particle metadata into star files for relion if you then
>> > want to use relion to process.
>> >
>> > % example code for cropping helical subtomograms
>> > model = dmodels.filament() % creates a workspace object 'model' of type
>> > filament
>> > model.addPoint([x1,y1,z1]) % adds startpoint [x1,y1,z1] to model
>> > model.addPoint([x2,y2,z2]) % adds intermediate/endpoint to model
>> > model.subunits_dphi = desired angular difference between subtomograms
>> > model.subunits_dz = desired spacing between subtomograms
>> > model.backboneUpdate() % creates a backbone along the helix
>> > model.updateCrop() % creates the cropping points for cropping
>> subtomograms
>> >
>> > table = dynamo_table_import(model) % creates table from cropping from
>> > tomogram
>> > dtcrop('/path/to/tomogram', table, 'output/path/here', sidelength) %
>> > crops subtomograms to defined output folder (sidelength refers to box
>> > size in pixels)
>> >
>> > There are also various very nice gui tools in dynamo for completing this
>> > if you prefer, including tools for picking particles from filaments in
>> > different ways :)
>> >
>> > https://wiki.dynamo.biozentrum.unibas.ch/w/index.php/Filament_model
>> >
>> > Hope this helps,
>> >
>> > Cheers,
>> >
>> > Alister
>> >
>> >
>> > On 31/05/2018 13:04, Sergey Nazarov wrote:
>> >> Dear list members,
>> >>
>> >> I have a question regarding extracting 3D helical subtomograms from
>> >> start-ends coordinates.
>> >> If this functionality has been implemented already?
>> >> In my case (RELION 2.1-beta-1) it gives an error
>> >> "Preprocessing::readCoordinates ERROR: Cannot extract 3D helical
>> >> subtomograms from start-end coordinates!"
>> >> And according to preprocessing.cpp (lines 567-568) it is not allowed
>> >> yet.
>> >> If provide segment coordinates, there is a "no prior information"
>> error.
>> >>
>> >> Thank you in advance.
>> >>
>> >> Best regards,
>> >>
>> >> Sergey Nazarov
>> >> Biozentrum, University of Basel
>> >>
>> >> ------------------------------------------------------------
>> ------------
>> >>
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>> >
>> >
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>> >
>>
>>
>> --
>> Sjors Scheres
>> MRC Laboratory of Molecular Biology
>> Francis Crick Avenue, Cambridge Biomedical Campus
>> Cambridge CB2 0QH, U.K.
>> tel: +44 (0)1223 267061
>> http://www2.mrc-lmb.cam.ac.uk/groups/scheres
>>
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>
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