[phenixbb] phenix.refine crash -- other error

[Peter Zwart]

Hi Ulrich,

You could try refining your structure in a primitive setting, this might 
  alleviate memory usage a bit (not sure though).

try

phenix.python $MMTBX_DIST/mmtbx/examples/reindex.py data.file=mydata.mtz 
  model.file=mymodel.pdb action=reindex standard_laws=niggli

You will get a new mtz file and a new pdb file. Unfortunately, the free 
flags are not copied over, so you would have to reindex those separately 
using iotbx.reflection_file_converter and read that file in separately 
in phenix.refine.

This might be a bit criptic, if so, let me know and I will post more 
details.

I am not sure this does the trick though, I hope Ralf or Pavel can give 
some suggestions.

Cheers

Peter




Ulrich Baumann wrote:
> Hi there,
> 
> if you remove the ANISOU card from the input pdb file, phenix will run fine
> ....sometimes not.
> 
> phenix.refine ( Version: 2007_01_24_2154) crashed for me as well: we have a
> rather large unit cell and good resolution. The program crashes reproducibly
> (see below) when using resolution limits better than 3 A, although sometimes
> this only occurs in the 2nd macrocycle.
> 
> Working crystal symmetry after inspecting all inputs:
>   Unit cell: (202.401, 202.401, 317.731, 90, 90, 120)
>   Space group: R 3 :H (No. 146)
> 
> 
> We have 2 GB memory and could stuff in more but maybe we can limit the memeory
> use in a different way?
> 
> 
> Thanks a lot for your help,
> 
> Ulrich
> 
> 
> ============================= ml refinement start =============================
> 
> 
>    ----------structure factors based statistics (before refinement)----------  
> 
> Traceback (most recent call last):
>   File "/usr/local/cci_apps/cci_apps_sources/phenix/phenix/command_line/refine.p
> y", line 5, in <module>
>     command_line.run(command_name="phenix.refine", args=sys.argv[1:])
>   File "/usr/local/cci_apps/cci_apps_sources/phenix/phenix/refinement/command_li
> ne.py", line 75, in run
>     call_back_after_monitor_collect=call_back_after_monitor_collect)
>   File "/usr/local/cci_apps/cci_apps_sources/phenix/phenix/refinement/driver.py"
> , line 1108, in run
>     log                     = log)
>   File "/usr/local/cci_apps/cci_apps_sources/phenix/phenix/refinement/strategies
> .py", line 174, in refinement_machine
>     abcd              = abcd)
>   File "/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/f_model.py", line 185, 
> in __init__
>     b_cart               = b_cart)
>   File "/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/f_model.py", line 466, 
> in update_xray_structure
>     f_mask = bulk_solvent_mask_obj.structure_factors(miller_set= self.f_obs)
>   File "/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/masks.py", line 97, in 
> structure_factors
>     flex.grid(fft_manager.m_real()).set_focus(fft_manager.n_real()))
> MemoryError
> 
> ----------------------------------------------------------
> -------------------------------------------------------
> Quoting Pavel Afonine <pafonine at lbl.gov>:
> 
>> Hi,
>>
>> this is known problem and it will be fixed ASAP; sorry for this.
>> This presumably happens because an atom selected to be refined as 
>> individual anisotropic is included into a TLS group.
>> I will let you know once the fixed version of CCI Apps is available.
>>
>> Pavel.
>>
>>
>>
>> Jianghai Zhu wrote:
>>> Hi,
>>>
>>> I was using phenix.refine from the latest cci apps bundle to do 
>>> tls+individual_sites+individual_adp refinement.  The program crashed 
>>> with the following error message.
>>>
>>>              ----------Target weights (before refinement)----------    
>>>        
>>>
>>> Traceback (most recent call last):
>>>   File 
>>> "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/command_line/refine.py", 
>>> line 5, in <module>
>>>     command_line.run(command_name="phenix.refine", args=sys.argv[1:])
>>>   File 
>>> "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/command_line.py",
>>> line 75, in run
>>>     call_back_after_monitor_collect=call_back_after_monitor_collect)
>>>   File 
>>> "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/driver.py", 
>>> line 1108, in run
>>>     log                     = log)
>>>   File 
>>> "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/strategies.py", 
>>> line 245, in refinement_machine
>>>     log                           = log)
>>>   File 
>>>
>> "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/weight_xray_chem.py",
>>
>>> line 222, in __init__
>>>     compute_gradients = True)
>>>   File "/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/restraints.py", 
>>> line 144, in energies_adp_aniso
>>>     xray_structure = xray_structure,
>>>   File 
>>> "/nfs/home/jzhu/cci_apps_sources/cctbx/cctbx/adp_restraints/__init__.py", 
>>> line 109, in __init__
>>>     self.check_flags(fl_i)
>>>   File 
>>> "/nfs/home/jzhu/cci_apps_sources/cctbx/cctbx/adp_restraints/__init__.py", 
>>> line 177, in check_flags
>>>     assert not fl.use_u_aniso()
>>> AssertionError
>>>
>>> Anyone has any idea what is happening?  Thanks.
>>>
>>> Jianghai
>>>
>>> +++++++++++++++++++++++++++++++
>>> Jianghai Zhu, Ph.D
>>> CBR Institute for Biomedical Research
>>> Department of Pathology
>>> Harvard Medical School
>>> 200 Longwood Ave., Boston, MA 02115
>>> Ph: 617-278-3211
>>> Fx: 618-278-3232
>>> +++++++++++++++++++++++++++++++
>>>
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>   
> 
>