[phenixbb] phenix-refine crash

[Carlos Frazao]

Hi,

After the  last model building of my protein I am not succeeding to 
further refine its structure, because phenix.refine crashes.

However, if I set  "main.number_of_macro_cycles=0" the job reaches its 
expected end and outputs a .pdb file.

If I set  "main.number_of_macro_cycles=1" the job crashes a few lines 
after the  log-file indication
" ============================== Exporting results 
=============================="
and produces an incomplete .pdb file with part of the header.

Alternatively, If I set  "main.number_of_macro_cycles=2" the job crashes 
during "MACRO_CYCLE 2 OF 2" after log-file indication
"              ----------Correcting NCS rotamer outliers----------
  Set U  69  GLU to tp10 rotamer"

followed by the error message :
"Traceback (most recent call last):
  File 
"/usr/local/phenix/phenix-dev-1391/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/phenix-dev-1391/phenix/phenix/refinement/command_line.py", 
line 161, in run
    call_back_handler=call_back_handler)
  File 
"/usr/local/phenix/phenix-dev-1391/phenix/phenix/refinement/driver.py", 
line 1659, in run
    ncs_manager             = self.ncs_manager).result
  File 
"/usr/local/phenix/phenix-dev-1391/phenix/phenix/refinement/strategies.py", 
line 170, in __init__
    ion_placement_manager = ion_placement_manager)
  File 
"/usr/local/phenix/phenix-dev-1391/phenix/phenix/refinement/macro_cycle.py", 
line 66, in __init__
    self.call(self.ncsrot,  "NCS rotamer correction")
  File 
"/usr/local/phenix/phenix-dev-1391/phenix/phenix/refinement/macro_cycle.py", 
line 101, in call
    func(prefix = prefix)
  File 
"/usr/local/phenix/phenix-dev-1391/phenix/phenix/refinement/macro_cycle.py", 
line 146, in ncsrot
    log         = self.log)
  File 
"/usr/local/phenix/phenix-dev-1391/phenix/phenix/refinement/misc.py", 
line 89, in ncs_rotamer_update
    log=log)
  File 
"/usr/local/phenix/phenix-dev-1391/cctbx_project/mmtbx/torsion_restraints/torsion_ncs.py", 
line 1111, in fix_rotamer_outliers
    key=key)
  File 
"/usr/local/phenix/phenix-dev-1391/cctbx_project/mmtbx/torsion_restraints/rotamer_search.py", 
line 178, in search
    assert rotamer == cur_rotamer
AssertionError"

I have been using built phenix-dev-1391 (I also checked phenix version 
1.8.2-1309 or built dev-1436, they crashed as well) x86_64-fc3, in  a 
machine running Ubuntu 10.04.4 LTS with Python 2.6.5.


I tried another machine, running Ubuntu 12.04 LTS with Python 2.7.3, and 
using built phenix-dev-1391 x86_64-fc3 I got at the end of the log-file:
"              ----------Correcting NCS rotamer outliers----------

Traceback (most recent call last):
  File 
"/usr/local/phenix/phenix-dev-1391/build/intel-linux-2.6/../../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/phenix-dev-1391/phenix/phenix/refinement/command_line.py", 
line 161, in run
    call_back_handler=call_back_handler)
  File 
"/usr/local/phenix/phenix-dev-1391/phenix/phenix/refinement/driver.py", 
line 1659, in run
    ncs_manager             = self.ncs_manager).result
  File 
"/usr/local/phenix/phenix-dev-1391/phenix/phenix/refinement/strategies.py", 
line 170, in __init__
    ion_placement_manager = ion_placement_manager)
  File 
"/usr/local/phenix/phenix-dev-1391/phenix/phenix/refinement/macro_cycle.py", 
line 66, in __init__
    self.call(self.ncsrot,  "NCS rotamer correction")
  File 
"/usr/local/phenix/phenix-dev-1391/phenix/phenix/refinement/macro_cycle.py", 
line 101, in call
    func(prefix = prefix)
  File 
"/usr/local/phenix/phenix-dev-1391/phenix/phenix/refinement/macro_cycle.py", 
line 146, in ncsrot
    log         = self.log)
  File 
"/usr/local/phenix/phenix-dev-1391/phenix/phenix/refinement/misc.py", 
line 89, in ncs_rotamer_update
    log=log)
  File 
"/usr/local/phenix/phenix-dev-1391/cctbx_project/mmtbx/torsion_restraints/torsion_ncs.py", 
line 1044, in fix_rotamer_outliers
    self.rotamer_search_manager.prepare_map(fmodel=fmodel)
  File 
"/usr/local/phenix/phenix-dev-1391/cctbx_project/mmtbx/torsion_restraints/rotamer_search.py", 
line 57, in prepare_map
    torsion_utils.prepare_map(fmodel=fmodel)
  File 
"/usr/local/phenix/phenix-dev-1391/cctbx_project/mmtbx/torsion_restraints/utils.py", 
line 771, in prepare_map
    not exclude_free_r_reflections))
  File 
"/usr/local/phenix/phenix-dev-1391/cctbx_project/mmtbx/map_tools.py", 
line 242, in fft_map
    symmetry_flags    = symmetry_flags)
  File 
"/usr/local/phenix/phenix-dev-1391/cctbx_project/cctbx/miller/__init__.py", 
line 3420, in fft_map
    f_000=f_000)
  File 
"/usr/local/phenix/phenix-dev-1391/cctbx_project/cctbx/miller/__init__.py", 
line 4236, in __init__
    conjugate_flag=True)
MemoryError"-


I did not succeed to find out what may I have done wrong with the model  
and/or params files
Any help is highly appreciated,

Carlos

-- 
**************************************
Dr. Carlos Frazao
Structural Biology Laboratory - 
Macromolecular Crystallography Unit
ITQB-UNL, Av Republica, Apartado 127
2781-901 Oeiras, P

Phone:  (351)-214469666    
FAX:    (351)-214433644
e-mail: frazao at itqb.unl.pt
        www.itqb.unl.pt