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

16 Mar 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 :
...
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
...
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",
...
...
185,
...
in __init__
    b_cart               = b_cart)
  File "/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/f_model.py",
Ulrich Baumann wrote:
line
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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