phenix.refine: Override 'Number of bonds with excessive lengths'
Dear All, Is there a way to override the phenix.refine Setup Restraints Manager, preventing phenix.refine from terminating if the model features a lot of excessive bond lenghts? Thanks, /Martin ========================== Set up restraints manager ========================== .... Bonds with excessive lengths: Distance model: 50.2364 (ideal: 1.525) ATOM 1336 C3' DC B 20 12.611 28.560 12.463 1.00 42.81 C ATOM 1338 C2' DC B 20 -11.801 15.989 54.531 1.00 42.03 C .... Sorry: Number of bonds with excessive lengths: 71 -- Martin Laurberg, PhD Noller Laboratory 225 Sinsheimer Laboratories University of California at Santa Cruz CA-95064 Santa Cruz USA Tel +1 (831) 459 35 84 Fax +1 (831) 459 37 37
Hi Martin,
Is there a way to override the phenix.refine Setup Restraints Manager, preventing phenix.refine from terminating if the model features a lot of excessive bond lenghts?
Not with a parameter, but you can force it like this: Edit the file $PHENIX/mmtbx/mmtbx/monomer_library/pdb_interpretation.py Look for these lines (around line 2628): raise Sorry("Number of bonds with excessive lengths: %d" % excessive_bonds.size()) Comment out: #raise Sorry("Number of bonds with excessive lengths: %d" % # excessive_bonds.size()) Ralf
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Martin.Laurberg -
Ralf W. Grosse-Kunstleve