Magdistortion

Hi,

I am trying to use mag distortion and I have high hopes for it because my box size is quite large (768^2). I have 2 questions:

1. What is the best way to convert relion stacks to frealign stacks and vise versa?

2. (The important one!) Does the package read all the images to RAM first? No matter what I do I run out of memory. Is there a way around this? I can split the stack but again I will need to use relion for that, hence, question 1!!!

Thanks!
Hamid

Good morning,

I have run mag_dist_est program and I got two sets of params (original Apix is 0.889):

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The following distortion parameters were found :-

Major Scale = 1.002
Minor Scale = 0.998
Distortion Angle = 109.1

Stretch only parameters would be as follows :-

Major Scale = 1.005
Minor Scale = 1.000
Distortion Angle = 109.1

Corrected Pixel Size = 0.887

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Hi Tim,
On our Krios I have performed the check for Mag distortions with gold images according to your paper and got the following result:

Distortion Angle = 19.6
Major Scale = 1.005
Minor Scale = 0.995
Stretch only parameters would be as follows :-
Distortion Angle = 19.6
Major Scale = 1.011
Minor Scale = 1.000
Corrected Pixel Size = 0.529
The Total Distortion = 1.10%

this post was deleted to avoid confusion.

Hi,

The table attached below from your paper has magnifications going down to 14kx. Does your camera have gold rings at that magnification (implying a <1.0 Å/pix pixel size)? If not how was the mag. distortion calculated and which 'powder diffraction' rings from what sample were used?

Additionally, do you have a graph of 'best resolution' vs. % distortion?

Kind Regards,
Duncan

Hi,

I am trying to estimate mag_distortion. I collected 20 micrographs from the gold grid in the super resolution mode. Each micrograph is of 50 frames, frames were aligned and summed. Gain reference correction was applied too. However, I get different values of Distortion angle for different combination of images used to calculate mag_distortion. e.g.

When Images 1-11 are used for the calculation, output is:

The following distortion parameters were found :-

Distortion Angle = 41.2
Major Scale = 1.006
Minor Scale = 0.994

Hi,

Hi:

I have tested mag_distortion_estimate and mag_distortion_correct on 16 aligned and summed micrographs that have nice ice rings. Both these programs seem to work quite well, thank you for writing the software and making in easily available!

Hi,

is there any problem in using images collected with energy filter for mag distortion determination? Would this bias the program?
Moreover, in the paper is mentioned polycrystalline gold with rings at ~2 and ~2.4 A. Would it be possible to use graphitized carbon grids with rings at 3.4A for mag with relatively lower pixel size?

Many thanks in advance,

Edoardo

Hi,

I was wondering how to verify the mag_distortion_correction result.

I did mag distortion estimation on an original image and the results were:
distortion angle 42.0
major scale 1.015
minor scale 0.985
total distortion 2.97%
stretch only parameters: 42 / 1.03 / 1 / 0.626

After doing mag distortion correction with the stretch only parameters, I did mag distortion estimation again on the corrected image, and the results were:
distortion angle 42.2
major scale 1.007
minor scale 0.993
total distortion 1.40%
stretch only parameters: 42 / 1.014 / 1 / 0.622