[phenixbb] phenix.refine with simulated annealing

zhangh1 at umbc.edu zhangh1 at umbc.edu
Fri Dec 17 16:43:32 PST 2010


Hi there,

I was trying to perform a SA refinement for PDB# 2VZ8 using the following
phenix script:

random_seed=2679941
phenix.refine 2VZ8.pdb 2vz8.mtz simulated_annealing=true
main.random_seed=${random_seed} output.prefix=${random_seed}
>${PDB}-phx-sa.log

where 2VZ8.pdb was downloaded from rcsb, and 2vz8.mtz was converted from
the cif file by ccp4-cif2mtz. But it ended up with:

*******************
=============================== refinement start
==============================

Traceback (most recent call last):
  File
"/users/hz9/TOOLS/PHENIX/phenix-1.6.4-486/phenix/phenix/command_line/refine.py",
line 11, in <module>
    command_line.run(command_name="phenix.refine", args=sys.argv[1:])
  File
"/users/hz9/TOOLS/PHENIX/phenix-1.6.4-486/phenix/phenix/refinement/command_line.py",
line 89, in run
    call_back_handler=call_back_handler)
  File
"/users/hz9/TOOLS/PHENIX/phenix-1.6.4-486/phenix/phenix/refinement/driver.py",
line 1182, in run
    call_back_handler       = call_back_handler)
  File
"/users/hz9/TOOLS/PHENIX/phenix-1.6.4-486/phenix/phenix/refinement/strategies.py",
line 229, in refinement_machine
    xray_structure = model.xray_structure,)
  File
"/users/hz9/TOOLS/PHENIX/phenix-1.6.4-486/phenix/phenix/refinement/strategies.py",
line 133, in extract_from_pdb_header
    xray_structure = xray_structure)
  File
"/users/hz9/TOOLS/PHENIX/phenix-1.6.4-486/cctbx_project/mmtbx/f_model.py",
line 302, in __init__
    twin_law_xyz = sgtbx.rt_mx(symbol=self.twin_law, r_den=12, t_den=144)
RuntimeError: cctbx Error: Parse error: unexpected character:
  NULL
************************

I tried another smaller system and it works well. Not sure what happens,
and thanks for any suggestion!

Hailiang




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