[Chimera-users] Chimera - mask after vop

[Ryan Harlich]

Hi Chimera team,

Is it possible to mask after vop. I got it to work in Chimera’s command line in the gui but when I run it from my python script it does not work. I am trying to change this working solution to this solution without ground truth:

WORKING SOLUTION
    #chimera_script.write('open ' + paths['input'] + '\n'
    #                     'open ' + paths['ground_truth'] + '\n'
    #                     'molmap #1 6 gridSpacing 1\n'
    #                     'volume #1.1 level 0.1\n'
    #                     'mask #0 #1.1\n'
    #                     'vop resample #2 onGrid #1.1\n'
    #                     'volume #3 save ' + paths['cleaned_map'])

NEW SOLUTION
    chimera_script.write('open ' + paths['input'] + '\n'
                         'vop gaussian #0 sDev 2\n'
                         'vop median #1 iterations 5 modelId #2.1\n'
                         'volume #2.1 level 0.1\n'
                         'mask #0 #2.1\n'
                         'vop resample #3 onGrid #2.1\n'
                         'volume #4 save ' + paths['cleaned_map'])

While mask after vop works with GUI command line it gets a NoneType error when doing this: subprocess.run(['/usr/local/bin/chimera', '--nogui', chimera_script.name]). It seems like this might be a bug of chimera? Since it tries to return None to a tuple and crashes. For some reason no triangles in the new surface with vop. Here is a snippet from the depthmask.py where it crashes.
[cid:image001.png at 01D525AB.830ADC20]


Thank you,

Ryan Harlich

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