[phenixbb] phenix.refine crash -- other error

Petrus H Zwart PHZwart at lbl.gov
Fri Mar 16 08:15:55 PDT 2007


This is very surprising. Not sure what happens actually.

Can you please go to the directory where you have the cci_apps sources located, specifically, this file:

/usr/local/cci_apps/cci_apps_sources/cctbx/cctbx/crystal/__init__.py

and grep for 

select_crystal_symmetry

Can you send me the build tag/version of cci_apps you installed? That might make it easier for me to find out exactly what is going on ...

or send me these files:
/usr/local/cci_apps/cci_apps_sources/cctbx/cctbx/crystal/__init__.py
/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/examples/reindex.py

Sorry for this,

Peter





----- Original Message -----
From: Ulrich Baumann <ulrich.baumann at ibc.unibe.ch>
Date: Friday, March 16, 2007 4:15 am
Subject: Re: [phenixbb] phenix.refine crash -- other error
To: PHENIX user mailing list <phenixbb at phenix-online.org>

> 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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