EMAN 2.99.72 e2spt_sgd_new.py error

[Raven Gonsoulin]

Hi all,

I have been getting a segmentation fault with the e2spt_sgd_new.py command when trying to apply helical symmetry to convnet-picked particles (e2spt_boxer_convnet.py). So far helical symmetry has only worked with particles I have manually picked and extracted as curves. I am not sure what is causing the segmentation fault as e2spt_sgd_new.py has worked with the exact same parameters I have used before (with the only difference being how the particles were picked/extracted).

Thanks,

Raven Gonsoulin
PhD Candidate
Boston University | Graduate Medical Sciences
Pharmacology, Physiology, and Biophysics

[Steve Ludtke]

Hi Raven,

e2spt_sgd_new.py is only used for making initial models. You shouldn't need to dump all of your data into it. You're just trying to get something that looks vaguely like your target so you can then run e2spt_refine_new.py   So, if you have a starting model from some of your particles, I wouldn't worry about debugging this issue...

If you do need to solve the problem, we'll need more info (this goes for any program which is crashing on you):

- The complete output of e2version.py run on the machine where the crash  is occuring

- The full command-line you ran (not just the name of the program) 

- The complete console output of the program including the crash itself

That's a starting point, and we may have an immediate answer, or need to ask followup questions. Segmentation faults _should_ never occur. When they do, it's almost always one of two things:

1) inconsistent software installation (mixed library versions or something). However, if the crash is data-dependent, then it's probably not this 

2) problem with the data. For example, if you try to process a particle stack where some of the particles are 64x64 and some are 256x256 pixels, then some programs may choke.

We're happy to help you work out what's happening, and hopefully you'll learn something which will help you next time.

cheers

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