Comments and questions about processing images with mag_distortion_estimate and correct.

Magnification questions

Hi, I am trying to correct micrographs collected from K2 Summit using mag_distortion serial programs. But I have faced some problems about magdistortion.
1. Can the micrographs (not crystalline areas, such as virus or proteins) be used for distortion estimation? I have tested some images from different types of grids with various samples. It seems that the major scale and minor scale are the same in the same batch of micrographs. But the distortion angles are quite different in the same batch.

Frame alignment


Do you perform mag distortion correction before or after drift correction/whole frame alignment? I used unblur to align my image stack and when I did the mag correction before alignment the power spectrum looked totally off, but it seemed normal after alignment and correction but the 3D refinement is 10 angstroms worse. Thanks!

Array is not properly allocated

I am trying to run Tim’s program to estimate if there is any
anisotropy in our scope and am getting an error array is not properly
allocated. I aligned with DM and created an aligned micrograph to put
into the program. Does the program require a stack of frames or is
there a problem with the mrc output from DM? Thanks.

Possible errors in pixel size

In the output rotational average file (my_amp_rot.mrc), is the bright ring (2.4A gold ring?) supposed to be fully visible within the mask if expert options are set to 'NO'?
In my test, at some magnifications, the ring is cut off by the inner circle of the mask. Does that indicate the pixel size I input is wrong? The ring becomes fully visible if I change the resolution limits in the expert options. Actually different resolution limits give me different results.
In addition to the results of estimation, is there a parameter that can indicate the confidence of the estimation?

Output for Relion 1.3


I'm trying to use the corrected CTF magnification with Relion 1.3 but there is no .log output which I can extract the values. Is there a way to generate these files from the final corrected CTF? Thanks!