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@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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