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CCPEM  June 2018

CCPEM June 2018

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Subject:

Re: Extracting 3D helical subtomograms from start-ends coordinates

From:

Sjors Scheres <[log in to unmask]>

Reply-To:

Sjors Scheres <[log in to unmask]>

Date:

Fri, 1 Jun 2018 09:22:22 +0100

Content-Type:

text/plain

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text/plain (86 lines)

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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-- 
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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