[phenixbb] problem with version 1.7.1-743 linux

Pavel Afonine pafonine at lbl.gov
Wed May 11 10:21:00 PDT 2011


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
>
> ******************************************************************************* 
>
> 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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