[3dem] FT artefacts from EPU .mrc files

[Schenk, Andreas]

Hi James,

I have seen these artefacts as well when running Gctf on the EPU average mrc files.
I think Gctf doesn't properly interpret the extended mrc header in these files and reads it as pixel data instead.

You can run:
e2proc2d.py --outmode uint16 --outnorescale in.mrc out.mrc

to strip the extended header out of the mrc file.
The alternative would be to run gctf on the motion corrected averages in case you do dose fractionation in EPU.

Best regards,
Andreas



> Hello all,
> 
> I am observing bizarre artefacts-vertical streaks and arrays of spots (attached)-in
> Fourier transforms calculated from EPU's averaged .mrc files during CTF
> estimation with Gctf v1.06 (via RELION-3.1.0). With Ctffind or after conversion to
> and from EMAN2's .hdf format, all seems normal.
> 
> Is there a known incompatibility between EPU's .mrc format and Gctf, or could
> these artefacts be caused by something else? Are there any alternative solutions
> to converting to and from .hdf?
> 
> Thank you,
> 
> James L. Kizziah, PhD | Cryo-EM Facility Manager Department of Microbiology
> UAB | The University of Alabama at Birmingham SHEL B40 | 1825 University Blvd |
> Birmingham, AL 35233 kizziah4 at uab.edu<mailto:kizziah4 at uab.edu> | Phone: (205)
> 975-3376 | Pronouns: he/him/his
> ************************************