[phenixbb] phenix.refine crash -- other error

Peter Zwart PHZwart at lbl.gov
Fri Mar 16 11:34:16 PDT 2007 

Good to know.

Let me know if the refinement is any faster.

Cheers

Peter


Ulrich Baumann wrote:
> Yop, that did it --- I sourced an old phenix setpaths and not the cci_apps.
> 
> Thanks a lot,
> 
> Ulrich
> 
> Quoting Peter Zwart <PHZwart at lbl.gov>:
> 
>> 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
>>>>>>> +++++++++++++++++++++++++++++++
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>> ------------------------------------------------------------------------
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>>>>>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>>>>>   
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>>>
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>

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