Hi Carlos,

The first error looks to be a problem with rotamer correction when using torsion NCS restraints. I'm not sure what is causing this crash in your case, but if you would send me your input pdb, mtz, and .eff file direct to my email, I will have a look.

The second crash looks like you've run out of memory on that particular machine. Perhaps one of the other developers would have an idea on that, but my guess is that the NCS crash is a problem either way.

Thanks,
Jeff


On Wed, Jul 31, 2013 at 2:20 PM, Carlos Frazao <frazao@itqb.unl.pt> wrote:
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@itqb.unl.pt
       www.itqb.unl.pt

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