[phenixbb] Error determining reference matches

[Pavel Afonine]

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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