[phenixbb] phenix.refine crash -- other error

[Ulrich Baumann]

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
> >   
> 


-- 
========================================
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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