[phenixbb] phenix.refine crash -- other error

Ulrich Baumann ulrich.baumann at ibc.unibe.ch
Fri Mar 16 05:14:58 PDT 2007


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
> >>>   
> > 
> > 
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
> 


-- 
========================================
Ulrich Baumann
University of Berne
ulrich.baumann at ibc.unibe.ch
phone + 41 31 631 4320/4343
fax + 41 31 631 4887

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