Hi, I am getting the following error when I run phenix.refine. How can I get rid of it? Katya =============================== refinement start ============================== ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- show_stack(1): /private/var/automount/nfs/programs/i386-mac/cciapps/2009_02_15_2320/cci_apps_sources/mmtbx/twinning/twin_f_model.py(1676) r_values show_stack(2): /private/var/automount/nfs/programs/i386-mac/cciapps/2009_02_15_2320/cci_apps_sources/mmtbx/twinning/twin_f_model.py(1837) r_work show_stack(3): /private/var/automount/nfs/programs/i386-mac/cciapps/2009_02_15_2320/cci_apps_sources/mmtbx/f_model.py(2249) __init__ show_stack(4): /private/var/automount/nfs/programs/i386-mac/cciapps/2009_02_15_2320/cci_apps_sources/mmtbx/twinning/twin_f_model.py(1139) info show_stack(5): /private/var/automount/nfs/programs/i386-mac/cciapps/2009_02_15_2320/cci_apps_sources/mmtbx/__init__.py(109) show_comprehensive show_stack(6): /private/var/automount/nfs/programs/i386-mac/cciapps/2009_02_15_2320/cci_apps_sources/phenix/phenix/refinement/strategies.py(280) refinement_machine show_stack(7): /private/var/automount/nfs/programs/i386-mac/cciapps/2009_02_15_2320/cci_apps_sources/phenix/phenix/refinement/driver.py(1121) run show_stack(8): /private/var/automount/nfs/programs/i386-mac/cciapps/2009_02_15_2320/cci_apps_sources/phenix/phenix/refinement/command_line.py(89) run show_stack(9): /programs/i386-mac/cciapps/2009_02_15_2320/cci_apps_sources/phenix/phenix/command_line/refine.py(16) <module> Floating-point error (Python call stack above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical. -- Ekaterina Heldwein, Ph.D. Assistant Professor Department of Molecular Biology and Microbiology Tufts University 136 Harrison Ave Boston, MA 02111 phone: 617-636-0858 fax: 617-636-0337 e-mail: [email protected]
Hi Katya,
I am getting the following error when I run phenix.refine. How can I get rid of it?
Quick answer: bash: export BOOST_ADAPTBX_FPE_DEFAULT=1 tcsh: setenv BOOST_ADAPTBX_FPE_DEFAULT 1 Then run the same command again. However, this particular failure is an indication of a bug in our code. I just looked at the code and have ideas what could be wrong, but I'm uncertain. It would be helpful if you could send me the inputs to reproduce the crash. Ralf
Just wondering, after some nice experience with kicked maps from a 'normal' case, I tried to get kicked maps for a twinned structure, and get the following...is this a known issue, is it possible to calculate kicked maps for a twinned refinement? Traceback (most recent call last): File "/Users/pkursula/cci-apps/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 "/Users/pkursula/cci-apps/cci_apps_sources/phenix/phenix/ refinement/command_line.py", line 101, in run map_manger.write_files() File "/Users/pkursula/cci-apps/cci_apps_sources/phenix/phenix/ refinement/driver.py", line 1256, in write_files symmetry_flags = maptbx.use_space_group_symmetry) File "/Users/pkursula/cci-apps/cci_apps_sources/mmtbx/maps.py", line 473, in __init__ b_sharp = b_sharp).fft_map File "/Users/pkursula/cci-apps/cci_apps_sources/mmtbx/maps.py", line 498, in __init__ r_free_flags = fmodel.r_free_flags, AttributeError: 'twin_model_manager' object has no attribute 'r_free_flags' bash-3.2$ Best regards, Petri --- Petri Kursula, Ph.D. Academy Research Fellow, Group Leader Docent of Neurobiochemistry Department of Biochemistry University of Oulu, Oulu, Finland [email protected] cc.oulu.fi/~pkursula www.biochem.oulu.fi/kursula ---
Hi Petri, sorry for the problem. No, currently you cannot compute "kick maps" using twinned data. It is our technical limitation that will be resolved at some point. Pavel. On 3/27/09 3:19 PM, Petri Kursula wrote:
Just wondering, after some nice experience with kicked maps from a 'normal' case, I tried to get kicked maps for a twinned structure, and get the following...is this a known issue, is it possible to calculate kicked maps for a twinned refinement?
Traceback (most recent call last): File "/Users/pkursula/cci-apps/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 "/Users/pkursula/cci-apps/cci_apps_sources/phenix/phenix/ refinement/command_line.py", line 101, in run map_manger.write_files() File "/Users/pkursula/cci-apps/cci_apps_sources/phenix/phenix/ refinement/driver.py", line 1256, in write_files symmetry_flags = maptbx.use_space_group_symmetry) File "/Users/pkursula/cci-apps/cci_apps_sources/mmtbx/maps.py", line 473, in __init__ b_sharp = b_sharp).fft_map File "/Users/pkursula/cci-apps/cci_apps_sources/mmtbx/maps.py", line 498, in __init__ r_free_flags = fmodel.r_free_flags, AttributeError: 'twin_model_manager' object has no attribute 'r_free_flags' bash-3.2$
Best regards, Petri
--- Petri Kursula, Ph.D. Academy Research Fellow, Group Leader Docent of Neurobiochemistry Department of Biochemistry University of Oulu, Oulu, Finland [email protected] cc.oulu.fi/~pkursula www.biochem.oulu.fi/kursula ---
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participants (4)
-
Katya Heldwein -
Pavel Afonine -
Petri Kursula -
Ralf W. Grosse-Kunstleve