After particles were picked, I should move the data to other computer, so I moved my job and reassign particles in new micrographs (same data but newly motion corrected and ctf estimated in new computer). There are no problems in particle extraction and other job, but almost all particles are considered as duplicated particle and rejected in 2d classification. Remove duplicated particle job has same result as 2D classification. Here are micrographs picture after remove duplicated particle. Please give me some inside to solve this problem.
If you re-did the most computationally expensive step (motion correction), why not just re-pick?
A workaround would be turn off duplicate particle removal. But then I would definitely recommend using the resulting good 2D classes to re-pick.
Although I’ll be honest, the two micrographs you show look far too concentrated for me to be happy with them if they were mine - and across most of the micrograph, it look like particles have aggregated.
I am trying to re-picking particles also but I just want to keep dose particle in case I miss some particle during re-picking (As you said particle distribution in my data is not good, so finding and picking minor view of protein are not much easier).
Those two micrographs are same micrographs but represent kept particle and rejected particle on them (upper one is kept particle) after remove duplicated particle. I forgot to mention it in text
