phenix.refine crash

Jianghai Zhu

25 Feb 2007 25 Feb '07

3:59 a.m.

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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Pavel Afonine

25 Feb 25 Feb

5:40 a.m.

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

13 Mar 13 Mar

5:06 p.m.

New subject: phenix.refine crash -- other error

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

Peter Zwart

7:07 p.m.

New subject: phenix.refine crash -- other error

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

14 Mar 14 Mar

2:49 p.m.

New subject: phenix.refine crash -- other error

Dear Peter, many thanks! Will try this -- I do not know about the FFT algorithm in phenix, but in CNS you could specify memory use and do calculations on a subgrid. Thi stakes more time but needs less memory. There is no cuh thing in phenix? many thanks again for your prompt help, Ulrich On Tue, 13 Mar 2007 20:07:46 +0100, Peter Zwart wrote:

...

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

16 Mar 16 Mar

12:14 p.m.

New subject: phenix.refine crash -- other error

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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Petrus H Zwart

3:15 p.m.

New subject: 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 +++++++++++++++++++++++++++++++

-------------------------------------------------------------

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

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

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

Ulrich Baumann

5:39 p.m.

New subject: phenix.refine crash -- other error

Files are attached -- hope I got the right ones.... Quoting Petrus H Zwart :

...

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 +++++++++++++++++++++++++++++++

-------------------------------------------------------------

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

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

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

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

Petrus H Zwart

19 Mar 19 Mar

6:13 p.m.

New subject: 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 :

...
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

...
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

...
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,

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

...
...
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

will run 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

...
...
...
abcd = abcd) File

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

...
...
...
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,

...
...
...
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

...
...
MemoryError

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

...
Hi,

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

...
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

flex.grid(fft_manager.m_real()).set_focus(fft_manager.n_real()))> this.> > > >> This presumably happens because an atom selected to be 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 > [email protected] > http://www.phenix-online.org/mailman/listinfo/phenixbb >

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

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

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

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

Peter Zwart

16 Mar 16 Mar

5:42 p.m.

New subject: phenix.refine crash -- other error

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 Ulrich Baumann wrote:

...

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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Jianghai Zhu
Pavel Afonine
Peter Zwart
Petrus H Zwart
Ulrich Baumann