[phenixbb] problem with version 1.7.1-743 linux

Nathaniel Echols nechols at lbl.gov
Thu May 12 08:05:29 PDT 2011

On Wed, May 11, 2011 at 1:11 PM, Daniel PANNE <panne at embl.fr> wrote:
> I get the following error only in 1.7.1-743 but not in 1.7_650.
> *******************************************************************************
> ERROR: Unused parameter definitions:
>  refinement.main.compute_optimal_errors (file "P1_refine_rigid.eff", line
> 257)
>  refinement.pdb_interpretation.peptide_link.use_finite_differences (file
> "P1_refine_rigid.eff", line 514)
>  refinement.secondary_structure.h_bond_restraints.substitute_n_for_h (file
> "P1_refine_rigid.eff", line 977)
> ...
> *******************************************************************************
> Sorry: Unused parameter definitions:
>  Please check the input file(s) for spelling errors and obsolete
>  parameter definitions.
>  To disable this error message, add
>    --unused_ok
>  to the command line arguments.

Sorry, most of these were my changes - I wanted to make the parameters
for configuring hydrogen bonding energy functions more general and not
specific to secondary structure (it will allow us more flexibility in
the future).  Like Pavel says, this tends to happen with new versions,
and it's easy to avoid, but the program stops because we want to make
sure users are aware of the changes.  FYI, if you've modified the
secondary structure restraint parameters, many of them moved to


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