[phenixbb] phenix.refine abort

[Pavel Afonine]

Hi,

try using "use_molprobity=false" which should disable the crashing step.
This is masking rather than solving the problem.

I can have a closer look if you send me files off list.

Pavel

On 8/21/14 10:44 PM, sujata halder wrote:
> Hi,
>
> I am trying to refine a protein with 60 chains (a T=1 virus; 5-3-2 
> symmetry) and each chain has 520 amino acids. I am using version 1.9 
> (Release tag: 1692). The job stopped midway and gave the error below 
> followed by "Cannot allocate memory". I have run a similar job (i.e 
> using a similar sized protein) before on an older version (version 
> 1.7) and that had worked.
> Looking at the error I can't really figure out if the problem is 
> related to installation or a missing module or something different 
> about the code.
>
> I can share my files off-list.
>
> Here is the error:
>
> ====================== XYZ individual (reciprocal space) ======================
>
>      R-FACTORS           RMSD     CLASH  RAMA  ROTA CBET WEIGHT    TARGETS
>   work  free  delta  bonds  angl                                  data   restr
> 28.80 29.29   0.49  0.016   1.6   11.9   0.8   7.4   60   none  0.093 160.8996
> Traceback (most recent call last):
>    File "/usr/local/phenix-1.9-1692/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 "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/command_line.py", line 163, in run
>      call_back_handler=call_back_handler)
>    File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/driver.py", line 1577, in run
>      reference_model_manager = self.reference_model_manager).result
>    File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/strategies.py", line 183, in __init__
>      ion_placement_manager = ion_placement_manager)
>    File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/macro_cycle.py", line 114, in __init__
>      self.call(self.xyzrec,   "XYZ individual (reciprocal space)")
>    File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/macro_cycle.py", line 142, in call
>      func(prefix = prefix)
>    File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/macro_cycle.py", line 374, in xyzrec
>      prefix         = prefix)
>    File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/xyz_reciprocal_space.py", line 204, in __init__
>      call_back=(len(trial_weights)==1))
>    File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/xyz_reciprocal_space.py", line 314, in try_weight
>      result = self.show(weight=wt, print_stats=print_stats, call_back=call_back)
>    File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/xyz_reciprocal_space.py", line 365, in show
>      molprobity_scores = self.main.use_molprobity)
>    File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/model.py", line 1341, in geometry_statistics
>      molprobity_scores  = molprobity_scores)
>    File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/model_statistics.py", line 99, in __init__
>      self.clashscore = clashscore(pdb_hierarchy=pdb_hierarchy).get_clashscore()
>    File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/validation/clashscore.py", line 133, in __init__
>      verbose=verbose)
>    File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/validation/clashscore.py", line 257, in __init__
>      self.run_probe_clashscore(self.h_pdb_string)
>    File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/validation/clashscore.py", line 341, in run_probe_clashscore
>      stdin_lines=pdb_string).raise_if_errors().stdout_lines
>    File "/usr/local/phenix-1.9-1692/cctbx_project/libtbx/easy_run.py", line 158, in __init__
>      close_fds=not subprocess.mswindows)
>    File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6-x86_64/base/lib/python2.7/subprocess.py", line 709, in __init__
>      errread, errwrite)
>    File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6-x86_64/base/lib/python2.7/subprocess.py", line 1222, in _execute_child
>      self.pid = os.fork()
> OSError: [Errno 12] Cannot allocate memory
> -------------------------------------------------------------------------------------------------------------
> Thanks,
> Sujata
>
>
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