Hi,
> on the RELION side the shifts and rotations in a particle STAR file are applied to the reference
> to align it with the particle
I don't know the tomography part of RELION, but at least in SPA,
Orientations (rlnAngleRot, rlnAngleTilt, rlnAnglePsi) in a STAR file rotate the reference into observations (i.e. particle image), while translations
(rlnOriginXAngstrom and rlnOriginYAngstrom) shifts observations into the reference projection.
https://relion.readthedocs.io/en/release-4.0/Reference/Conventions.html#orientations
Best regards,
Takanori Nakane
On 2022/06/10 19:31, Alister Burt wrote:
> Hi Mat,
>
> I’m not sure about the emClarity side of things but on the RELION side the shifts and rotations in a particle STAR file are applied to the reference
> to align it with the particle. This means that to get the actual position in the tomogram you need to negate these shifts.
>
> e.g.
>
> new_x_position = rlnCoordinateX - ( rlnOriginXAngst / pixelsize )
>
> Hope that helps you move forwards a bit.
>
> Cheers,
>
> Alister
>
>> On 10 Jun 2022, at 11:15, McLaren, Mathew <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>>
>> Hi all,
>>
>> I am working with an STA dataset, converting it from Relion 3 into emClarity. I have previously combined the XYZ shifts and Euler angles of a PEET
>> run with the original particle picks with a reasonable reconstruction in emClarity, but if I do the same with Relion then the map is just noise. I
>> tried with just the original XYZ coordinates (no rlnOriginXYZAngst applied) and the Relion Euler angles I get my particle, albeit with a low resolution.
>> I have been combining the columns as follows for X, Y and Z:
>> new_position = rlnCoordinateX + ( rlnOriginXAngst / pixelsize )
>>
>> However, I noticed on the conventions page these sentences:
>>
>> The origin is the first element in the 2D array of an MRC file. The origin is displayed at the upper-left corner inrelion(other programs might
>> display in other ways).
>>
>> I then tried subtracting Y instead of adding as I thought the sign may be inverted on the Y-axis but this also didn't give a good reconstruction
>> either. I was wondering if anyone could advise the correct way of combining the rlnCoordinateXYZ and rlnOriginXYZAngst values together so I can
>> troubleshoot this issue.
>>
>> Cheers,
>>
>> Mat
>>
>> ----------
>>
>> Dr Mathew McLaren
>> TEM Experimental Officer
>> Living Systems Institute
>> University of Exeter
>> T: +44(0)1392 72*7468*
>> E:[log in to unmask] <mailto:[log in to unmask]>
>>
>> My pronouns are he / him / his.
>>
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