Re: [phenixbb] phenix.refine crash -- other error

16 Mar 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 :
...
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 :
...
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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-- 
========================================
Ulrich Baumann
University of Berne
[email protected]
phone + 41 31 631 4320/4343
fax + 41 31 631 4887

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