[phenixbb] phenix.refine crash -- other error

Peter Zwart PHZwart at lbl.gov
Fri Mar 16 10:42:47 PDT 2007 

Hi Ulrich,

Please make sure that the phenix.python used is actually the 
phenix.python you installed with cci_apps.

The behavoir seen might be due to using an other phenix.python 
installation (on that loads in old python libraries). This can be 
avoided by making sure that the last crystallographic package sourced in 
your .chsrc file, is the latest phenix/cci_apps installation.

A which phenix.python might give a clue what is run, and hitting the tab 
key or CRTl-D after typing phenix.refine might auytocomplete or give a 
list of possibilities.

Let me know what happened.


Peter









Ulrich Baumann wrote:
> Hi Peter,
> 
> I hate to bother you guys with this but ....
> 
> dcb-macbeth:[lip3] > phenix.python
> /usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/examples/reindex.py
> data.file=lip_r3_1.8A.mtz model.file=in.pdb action=reindex standard_laws=niggli
> #phil __OFF__
> =================
>     REINDEX      
> A reindexing tool
> =================
> 
> Traceback (most recent call last):
>   File "/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/examples/reindex.py",
> line 468, in ?
>     reindex_utils(sys.argv[1:])
>   File "/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/examples/reindex.py",
> line 260, in reindex_utils
>     combined_xs = crystal.select_crystal_symmetry(
> AttributeError: 'module' object has no attribute 'select_crystal_symmetry'
> 
> 
> I seem to hae to set a spacegroup? Sorry, I could not find a documentation for
> the reindex utility.
> 
> Many thanks,
> 
> Ulrich
> 
> Quoting Peter Zwart <PHZwart at lbl.gov>:
> 
>> 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
>>>>>   
>>>
>> _______________________________________________
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>>
> 
>

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