Hi, I’ve obtained some decent helical 2D classes and I would like to compare their power spectra to see if they have the same helical symmetry as well as estimate their symmetry parameters. I can’t seem to figure out how to get their power spectra from cryosparc.
I’m wondering if it is possible to get the power spectra of 2D classes in cryosparc, and if not, what else I can try to get the power spectra. I’d appreciate any suggestion. Thank you so much!
With some modifications described below, refer to my previous response in this thread here: High resolution image of 2D classification
That thread was specific for just viewing the 2D class averages, but either method recommended (EMAN2 or FIJI) allows you to view the power spectrum also.
FIJI would be easiest. It will open the .mrc file from cryosparc as a stack of 2D images. You can scroll to the image you want the spectrum for. Then you can select Process->FFT->FFT to calculate the FFT. You can save images in any format you desire.
EMAN will do this also, with the command (no quotes) “e2display.py --singleimage inputFile.mrc” which will open the class averages as a stack of 2D images. You can scroll through the stack with the up/down arrows. Then middle click (or option click (on a Mac)) on the image and in the window that pops up you can select “Amp” to show the FFT amplitude. You will probably also need to adjust the contrast of the FFT, either with Autocontrast, or with the sliders. The only way (I know) to save the FFT from e2display.py is to capture a screenshot, but if the magnification is set to 1, the pixel resolution will be correct. Oh, of course, EMAN will calculate and save the FFT directly, I’m sure, I just don’t know the exact command off the top of my head. Check the documentation. YMMV.
Thank you so much @rj.edwards ! I will give that a try.