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

Hi Ulrich, As far as I understand, you have solved the problem by sourcing the proper version of cci_apps. The files you send me look (actually glancing) fine and were not the issue. Cheers Peter ----- Original Message ----- From: Ulrich Baumann Date: Monday, March 19, 2007 9:29 am Subject: Re: [phenixbb] phenix.refine crash -- other error To: PHENIX user mailing list

Files are attached -- hope I got the right ones....

Quoting Petrus H Zwart :

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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

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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

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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 ?

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reindex_utils(sys.argv[1:]) File

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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 :

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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

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more

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details.

I am not sure this does the trick though, I hope Ralf or Pavel can give some suggestions.

Cheers

Peter

Ulrich Baumann wrote:

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Hi there,

if you remove the ANISOU card from the input pdb file,

"/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/examples/reindex.py",line> 260, in reindex_utils post phenix

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fine

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....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

will run limit the

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memeory

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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>

...

...

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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

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call_back_after_monitor_collect=call_back_after_monitor_collect)>

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File

"/usr/local/cci_apps/cci_apps_sources/phenix/phenix/refinement/driver.py">> > , line 1108, in run

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log = log) File

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abcd = abcd) File

"/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/f_model.py",

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in __init__ b_cart = b_cart) File "/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/f_model.py",

"/usr/local/cci_apps/cci_apps_sources/phenix/phenix/refinement/strategies>> > .py", line 174, in refinement_machine line> > > 185, line> > > 466,

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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

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MemoryError

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---------------------------------------------------------- ------------------------------------------------------- Quoting Pavel Afonine :

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Hi,

this is known problem and it will be fixed ASAP; sorry for

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refined as

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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

flex.grid(fft_manager.m_real()).set_focus(fft_manager.n_real()))> this.> > > >> This presumably happens because an atom selected to be program

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crashed

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> with the following error message. > > ----------Target weights (before refinement)-

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------

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> > > Traceback (most recent call last): > File >

"/nfs/home/jzhu/cci_apps_sources/phenix/phenix/command_line/refine.py",

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> 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

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call_back_after_monitor_collect=call_back_after_monitor_collect)>

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File >

"/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/driver.py",

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> line 1108, in run > log = log) > File >

"/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/strategies.py",>>

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> line 245, in refinement_machine > log = log) > File >

"/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/weight_xray_chem.py",>> >>

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> 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",>>

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> line 109, in __init__ > self.check_flags(fl_i) > File >

"/nfs/home/jzhu/cci_apps_sources/cctbx/cctbx/adp_restraints/__init__.py",>>

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> 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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> > _______________________________________________ > phenixbb mailing list > [email protected] > http://www.phenix-online.org/mailman/listinfo/phenixbb >

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

------------------------------------------------------ This mail was sent through IMP at http://mail.unibe.ch