[phenixbb] phenix.refine: Override 'Number of bonds with excessive lengths'

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Mon Aug 4 12:46:57 PDT 2008


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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