Hi Daniel, some parameters may change or become obsolete in newer versions of PHENIX. So if you run a newer version of phenix.refine using a parameter file created with older version there is a good chance of getting the error like the one below. If you are absolutely certain that the quoted parameters are ok to ignore then you can just run phenix.refine with an additional keyword "--unused_ok", which will disable that error message and will let phenix.refine continue. However, in general it is a good idea to create a new parameter file every time you update PHENIX and see an error like this. "--diff-params" may be helpful to find differences between your custom parameter file and the default settings. Pavel. On 5/11/11 10:11 AM, Daniel PANNE wrote:

I get the following error only in 1.7.1-743 but not in 1.7_650. Any idea? Thanks, Daniel

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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)

refinement.secondary_structure.h_bond_restraints.restrain_initial_values (file "P1_refine_rigid.eff", line 983) refinement.secondary_structure.h_bond_restraints.sigma (file "P1_refine_rigid.eff", line 984) refinement.secondary_structure.h_bond_restraints.slack (file "P1_refine_rigid.eff", line 985) refinement.secondary_structure.h_bond_restraints.h_o_distance_ideal (file "P1_refine_rigid.eff", line 986) refinement.secondary_structure.h_bond_restraints.h_o_distance_max (file "P1_refine_rigid.eff", line 987) refinement.secondary_structure.h_bond_restraints.n_o_distance_ideal (file "P1_refine_rigid.eff", line 988) refinement.secondary_structure.h_bond_restraints.n_o_distance_max (file "P1_refine_rigid.eff", line 989) *******************************************************************************

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.

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