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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