[phenixbb] Error determining reference matches

Jeff Headd jjheadd at lbl.gov
Sat Aug 31 07:01:26 PDT 2013


Hi Dan,

I agree with Pavel, we'll really need to see your files to be able to
figure out what is going on. Something is going wrong with the alignment
routine that is used to decide residue matching for reference restraints,
but without seeing the files it's hard to speculate as to why.

If you could send your files to me or Pavel (directly, not to the list)
we'll be able to sort out what is going wrong.

Thanks,
Jeff


On Fri, Aug 30, 2013 at 11:46 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

>  Hi Dan,
>
> the only way we can help (= debug the problem, fix it or/and suggest a
> work-around) is if we can reproduce it here locally. To do this we need all
> inputs and commands necessary to reproduce the refinement run that crashed.
> Please send files to me (not to whole mailing list) and I will look myself
> or redirect to a respective developer.
>
> Thanks,
> Pavel
>
>
> On 8/30/13 4:32 PM, Dan McNamara wrote:
>
>  Hi all,
>
> I am encountering a strange crash when running phenix.refine through the
> command line with reference model restraints turned on. The references
> point to two different PDB files, one labeled as chain A and one labeled as
> chain B.
>
> This error occurs whether I have my refinement model in P1 with 192 chains
> or P2(1) with 96 chains. The chains are A-EZ (192) or A-BH (96). It appears
> to fail to align the reference models to the sequences in the refinement
> model. This error does not occur with other smaller target structures under
> 25 chains and reference models used with the same installation of phenix.
>
>  I am hoping for any advice on why this might be happening or how I might
> get around it.
>
>  ================== Extract refinement strategy and selections
> =================
>
>  Refinement flags and selection counts:
> individual_sites = True (401472 atoms)
> torsion_angles = False (0 atoms)
> rigid_body = True (401472 atoms in 192 groups)
> individual_adp = False (iso = 0 aniso = 0)
> group_adp = True (201984 atoms in 25824 groups)
> tls = False (0 atoms in 0 groups)
> occupancies = False (0 atoms)
> group_anomalous = False
>
>  n_use = 401472
>  n_use_u_iso = 401472
> n_use_u_aniso = 0
> n_grad_site = 0
> n_grad_u_iso = 0
> n_grad_u_aniso = 0
> n_grad_occupancy = 0
> n_grad_fp = 0
> n_grad_fdp = 0
>  total number of scatterers = 401472
> *** Adding Reference Model Restraints ***
> determining reference matches automatically...
> Traceback (most recent call last):
> File
> "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/refine.py",
> line 11, in <module>
> command_line.run(command_name="phenix.refine", args=sys.argv[1:])
> File
> "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/phenix/phenix/refinement/command_line.py",
> line 92, in run
> master_params=customized_master_params)
> File
> "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/phenix/phenix/refinement/driver.py",
> line 501, in __init__
> log=self.log)
> File
> "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/cctbx_project/mmtbx/torsion_restraints/reference_model.py",
> line 147, in __init__
> self.get_reference_dihedral_proxies()
> File
> "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/cctbx_project/mmtbx/torsion_restraints/reference_model.py",
> line 460, in get_reference_dihedral_proxies
> log=self.log)
> File
> "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/cctbx_project/mmtbx/torsion_restraints/reference_model.py",
> line 323, in process_reference_groups
> moving_chain = mod_h)
> File
> "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/cctbx_project/mmtbx/torsion_restraints/utils.py",
> line 426, in _ssm_align
> ssm_alignment = ccp4io_adaptbx.SSMAlignment.residue_groups(match=ssm)
> File
> "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/ccp4io_adaptbx/__init__.py",
> line 215, in residue_groups
> return cls( match = match, indexer = indexer )
> File
> "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/ccp4io_adaptbx/__init__.py",
> line 176, in __init__
> self.pairs.append( ( get( f, indexer1 ), get( s, indexer2 ) ) )
> File
> "/auto_nfs/joule2/programs/phenix/phenix-installer-dev-1457/phenix-dev-1457/ccp4io_adaptbx/__init__.py",
> line 173, in get
> assert identifier in indexer, "Id %s missing" % str( identifier )
> AssertionError: Id ('A', 1, ' ') missing
>
>  Best,
> Dan
>
>
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