On 10 Jun 2022, at 11:15, McLaren, Mathew <[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 in relion (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 727468

E: [log in to unmask]

My pronouns are he / him / his.

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