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

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 Date: Friday, March 16, 2007 4:15 am Subject: Re: [phenixbb] phenix.refine crash -- other error To: PHENIX user mailing list

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

...

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

Ulrich Baumann wrote: 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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