issues found in distributed isostructure by Randy
Just tried to do a quick test of phenix.voyager.isostructure, using a crystal form I ran into with Aiwu’s data.
phenix.fetch_pdb —mtz 3ldi
phenix.voyager.isostructure reflections=3ldi.mtz
It found 3ldi at the top of the list and then gave a total of 100 nearest hits, but then failed like this:
(<class 'IndexError'>, IndexError('list index out of range'), <traceback object at 0x14c87a640>)
Traceback (most recent call last):
File "/Users/randy/phenix/phenix_bootstrap_dev/modules/phaser_voyager/command_line/../src/Voyager/Actions/isostructure_search.py", line 170, in run
output = self.isostructure_search(self.argsparse)
File "/Users/randy/phenix/phenix_bootstrap_dev/modules/phaser_voyager/command_line/../src/Voyager/Actions/isostructure_search.py", line 383, in isostructure_search
ic = simple_tools.Intensity_Correlation(mtz, logger=self.logger)
File "/Users/randy/phenix/phenix_bootstrap_dev/modules/phaser_voyager/command_line/../src/Voyager/MDSLibraries/simple_tools.py", line 4862, in __init__
mi1[1], print_all=True, pad=" ")
File "/Users/randy/phenix/phenix_bootstrap_dev/modules/phaser_voyager/command_line/../src/Voyager/MDSLibraries/simple_tools.py", line 2663, in findIndexingAlternatives
assert (reindexing[0].IsIdentity()) # 1st one should be h,k,l
IndexError: list index out of range
An exception of type IndexError occurred. Message:
('list index out of range',)
Thread complete
Also, bizarrely, the first time I ran it without arguments to see the command-line options, I got a warning message:
phenix.voyager.isostructure
/Users/randy/phenix/phenix_bootstrap_dev/modules/phaser_voyager/command_line/../src/Voyager/MDSLibraries/javascript_code_for_trees.py:10133: DeprecationWarning: invalid escape sequence \s
"""
However, when I tried the same later there was no error message!
Apart from the crash, I think that the default should be only to return the entries within the Niggli cone distance limit (6 in this case) and maybe say how many more there are within whatever larger limit it was looking at.