relion_prepare_subtomograms.py crash under special case

[bforsbe]

Originally reported by: Lu Gan (Bitbucket: lu_gan, GitHub: Unknown)

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The current version of this script will fail to create the particles_subtomo.star file if SkipCTFCorrection = True and Relion2 = True.

Under this condition, the script does not create the directory OutputDir/results. There's probably a more elegant solution, but I was able to fix this problem by inserting this one-liner between lines 388 and 389:

#!python
      os.system('mkdir %s' %(OutputDir + 'results'))

Lines 388 - 390 now read:

#!python
    if Relion2 == True:
      os.system('mkdir %s' %(OutputDir + 'results'))
      outputstarname_read =  OutputDir + 'results/micrographs_ctf.star'

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• Bitbucket: https://bitbucket.org/tcblab/relion2-beta/issue/154

[biochem-fan]

We will not fix this script. We will have a completely new CryoET pipeline in the next major update.