Memory problem with Magdistortion

Submitted by hr13b on Sat, 2018-06-23 16:25

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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

timgrant Mon, 2018-06-25 10:42

Hi Hamid,

1. If you use our new software package cisTEM (www.cistem.org) - then you can import / export between those formats. cisTEM also has magnification distortion correction integrated within the processing workflow.
2. If you are using mag_distortion_correct, then it does not load the images into memory, it reads one image at a time, corrects it for the specified parameters and writes out the corrected image. Typically, you would use this program to correct your raw data at the very beginning of processing. You can correct the particle stack, but if you do that then your defocus values will no longer be accurate, as the distortion appears as astigmatism, so defocus parameters estimated on images that were not corrected will be wrong after correction. This assumes you already know the distortion parameters for your microscope. If you do not, you need to run mag_distortion_estimate. This program is intended to be run on a stack of 10-20 images of different areas of a gold covered diffraction grating, taken at the magnification you want to estimate the parameters for.

Which program are you running?

Cheers,

Tim