Negative staining processing without CTF

closed

#1

Dear All,
I have a images from negative staining taken close to focus, and therefore it seems that both CTFfind and GCTF do fail to do any CTF estimation. In these conditions, I would not know why CTF estimation is needed. But because I can’t get the CTF parameters, processing with cryosparc is not possible. Would it be possible to implement in cryosparc a function to ignore the CTF estimation, if such functionality would be useful for the community?
Thank you and best wishes,
Jacopo


#2

I am also unable to get past 2D classification with negative stain. I can pick manually particles but if I want to then do 2D classification the particles are black and also the job fails with the following message

" File “/mnt/data1/App/cryosparc/cryosparc2/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/numpy/lib/function_base.py”, line 505, in histogram
‘range parameter must be finite.’)
ValueError: range parameter must be finite."


#3

@GMG You need to flip the data sign (or select “negative stain” during I think the Extraction job).

However, Template Picking with these classes appears to still flip the sign during the search, thus everything except the particles are picked!