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 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 input and output 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,