[phenixbb] reference model restrain error

[Jeff Headd]

Hi Stephan,

Sorry for the trouble. At some point we switched to using SSM
alignment to match the reference model to the working model, and it is
the SSM alignment algorithm that is producing the error. Does your
reference model or working model contain a residue position with more
than one amino acid type? The error message suggests that this may be
the case and that the two residues are not formatted with
differentiable insertion codes.

If you could send me your coordinate files (both working model and
reference) off-list it would help to debug the problem more quickly.

Thanks,
Jeff

2011/11/23 Stephan Barden <stephan.barden at uni-bielefeld.de>:
> Dear all,
>
> I'm facing a problem with a fresh (yesterday) installation of phenix
> 1.7.2-869 refining a structure with 6 molecules per ASU at 3.25 A and using
> a different reference structure with 1 mol/ASU at higher resolution. I wrote
> an additional parameter file to assign the reference model to each of the
> six molecules, which worked well with an older version of phenix. After the
> upgrade neither taking the additional parameter file, nor auto alignment
> worked for me. The error comming up is always:
>
>
> RuntimeError : Duplicate sequence number and insertion code.
> Traceback:
>  File "/sw/phenix-1.7.2-869/cctbx_project/libtbx/thread_utils.py", line 229,
> in run
>    return_value = self._target(self._args, self._kwargs, self._c)
>
>  File "/sw/phenix-1.7.2-869/cctbx_project/libtbx/runtime_utils.py", line 72,
> in __call__
>    result = self.target()
>
>  File "/sw/phenix-1.7.2-869/phenix/phenix/refinement/runtime.py", line 67,
> in __call__
>    call_back_handler=callback)
>
>  File "/sw/phenix-1.7.2-869/phenix/phenix/refinement/command_line.py", line
> 75, in run
>    overwrite = command_line_interpreter.command_line.options.overwrite)
>
>  File "/sw/phenix-1.7.2-869/phenix/phenix/refinement/driver.py", line 209,
> in __init__
>    log=self.log)
>
>  File
> "/sw/phenix-1.7.2-869/cctbx_project/mmtbx/torsion_restraints/reference_model.py",
> line 145, in __init__
>    self.get_reference_dihedral_proxies()
>
>  File
> "/sw/phenix-1.7.2-869/cctbx_project/mmtbx/torsion_restraints/reference_model.py",
> line 611, in get_reference_dihedral_proxies
>    log=self.log)
>
>  File
> "/sw/phenix-1.7.2-869/cctbx_project/mmtbx/torsion_restraints/reference_model.py",
> line 398, in process_reference_groups
>    raise e
>
> Has anyone observed a similar problem? Are there any suggestions?
>
> Thanks,
> StephanB.
>
>
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