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.
> Hi Sergey,
> Not sure if this has been implemented in relion, but it's easy to do in
> 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
> 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
> 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 :)
> Hope this helps,
> 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
>> 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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