Hi all,
I have run the tutorial completely and had no problems with the software working. However, when I imported my own .mrc still images from a pre-existing dataset, the program doesn't seem to like it. It will calculate CTF values, but when I move on to particle selection and select the preview button, the GUI crashes giving a Master Socket Disconnect and segmentation fault error. I'm not sure if this is an issue with cisTEM or if it just doesn't like my images. Is there a straightforward way to diagnose this?
Best,
Tori
Hi Tori,
Sorry you're running into problems. The fact that your images make the picker crash but not CTF estimation is quite unusual. Could you please put a representative image causing this up on a website that I could download from? You may even be able to attach it to your existing post here (but I don't think you can attach files to replies) - if not, anything like dropbox would do. I'll then give it a spin and let you know what I find.
Cheers,
Alexis
Good morning Alexis!
I spent some time thinking about this last night and realized it was because the 2D images I was importing had to go through a conversion process from .dm3 to .pif to .mrc file types to be usable in cisTEM. However, this did not include the power spectra that are included when converting from .mrc movie files. I resolved this issue using the autopp UNIX wildcard in the auto3dEM software suite via the ctffind4 option to generate the power spectra for my .pif micrographs, then import all *_pow.mrc power spectra and all *.mrc converted images. Then, after I ran the CTF selection in cisTEM, I was able to complete particle picking without the GUI crashing.
In summary, if you import 2D .mrc images (not films), you have to include the power spectra, otherwise the GUI will crash when you move beyond the ctf file generation step.
If you would still like for me to send you those images, I am happy to do so. Thanks again for your help, I am really loving my experience with cisTEM so far. Congrats on all your hard work!
Best wishes,
Tori