[phenixbb] phenix.find_blobs command problems
oleg at quantumbioinc.com
oleg at quantumbioinc.com
Fri Jan 20 07:22:09 PST 2017
I tried to use phenix.find_blobs command but it ended up with a Python crash. Any thoughts?
Thanks a lot
Oleg
P.S. I tried to attached the input files but it seems to be over the allowed message size
phenix.find_blobs protein_pdb_file_name=1LRI-H_refine_001.pdb map_coeffs_file_nam=1LRI-H_refine_001.mtz
#phil __OFF__
banner
#phil __ON__
find_blobs {
input {
protein_pdb_file_name = "1LRI-H_refine_001.pdb"
data_file_name = None
map_coeffs_file_name = "1LRI-H_refine_001.mtz"
}
output {
blob_number = None
}
options {
random_seed = 0
density_contour = 2.5
}
}
#phil __END__
Random number seed: 3628800
Adding PDB model from 1LRI-H_refine_001.pdb
Traceback (most recent call last):
File "/home/oleg/phenix-1.11.1-2575/build/../modules/phenix/phenix/command_line/find_blobs.py", line 169, in <module>
run( tuple(args) )
File "/home/oleg/phenix-1.11.1-2575/build/../modules/phenix/phenix/command_line/find_blobs.py", line 162, in run
rc = execute(params)
File "/home/oleg/phenix-1.11.1-2575/build/../modules/phenix/phenix/command_line/find_blobs.py", line 98, in execute
bfo.setup_blobs(working_params.options.density_contour)
File "/home/oleg/phenix-1.11.1-2575/modules/phenix/phenix/ligands/blob_finding_class.py", line 25, in setup_blobs
contour=contour,
File "/home/oleg/phenix-1.11.1-2575/modules/phenix/phenix/ligands/DensityBlobsClass.py", line 14, in __init__
self.map_residue = self.data_map["fofc_fft_map"] # fft map
TypeError: 'fft_map' object has no attribute '__getitem__'
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