search

xuewuzhang-UTSW / PyHI

A python-based GUI for helical indexing
4 stars 1 forks source link

Average_power_spec_calc_v03.py #2

Closed lorago92 closed 2 years ago

lorago92 commented 2 years ago

Hello, I'm running Average_power_spec_calc_v03.py but I get the following message

Traceback (most recent call last): File "Average_power_spec_calc_v03.py", line 84, in fft_average=fft_stack/process_count ZeroDivisionErrorr: division by zero

I am using a particles.star file as input (from Class2D/Select/ job in relion 3.1) so I don't get the problem here.

Cheers Lorenzo

xuewuzhang-UTSW commented 2 years ago

Hi Lorenzo, Based on the error message, it seems like that the script did not successfully get the "process_count" (the number of particles to be processed) from your input files, hence the "division by zero" problem. This suggest that it did not find the particle stack files (.mrcs). Are you running the script in the directory where the "particles.star" file is? Can you paste the command you used? Thanks, Xuewu

lorago92 commented 2 years ago

Here the command:

python Average_power_spec_calc_v03.py -i /data/MizunoLab/agostinil2/NIHCryoem/singleparticle/Processing/3E/Select/job112/particles.star -d /data/MizunoLab/agostinil2/NIHCryoem/singleparticle/Processing/3E/Select/job112

No, I am actually running the job from another directory. Should I run it from the relion folder?

xuewuzhang-UTSW commented 2 years ago

I see what's the issue: your command after the "-d" does not point to the correct directory to the ".mrcs" particle stack directory, instead it points to the "Select/job112" directory (which only has the 2D class images, not the actual particles). The particle stacks should be under one of your "Extract" jobs (whichever one you used for your 2D class run). You can find exactly where that directory is in your "particles.star" file. After the header of the file, you should see that each line represents data for one particle. Look for something like "00007@Extract/job033/Movies/XXXX.mrcs". Xuewu

lorago92 commented 2 years ago

It runs now. Thank you. Lorenzo