<div dir="ltr">Hi Carlos,<div><br></div><div>The first error looks to be a problem with rotamer correction when using torsion NCS restraints. I'm not sure what is causing this crash in your case, but if you would send me your input pdb, mtz, and .eff file direct to my email, I will have a look.</div>
<div><br></div><div>The second crash looks like you've run out of memory on that particular machine. Perhaps one of the other developers would have an idea on that, but my guess is that the NCS crash is a problem either way.</div>
<div><br></div><div>Thanks,</div><div>Jeff</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Jul 31, 2013 at 2:20 PM, Carlos Frazao <span dir="ltr"><<a href="mailto:frazao@itqb.unl.pt" target="_blank">frazao@itqb.unl.pt</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<br>
After the �last model building of my protein I am not succeeding to further refine its structure, because phenix.refine crashes.<br>
<br>
However, if I set �"main.number_of_macro_cycles=<u></u>0" the job reaches its expected end and outputs a .pdb file.<br>
<br>
If I set �"main.number_of_macro_cycles=<u></u>1" the job crashes a few lines after the �log-file indication<br>
" ============================== Exporting results ==============================<u></u>"<br>
and produces an incomplete .pdb file with part of the header.<br>
<br>
Alternatively, If I set �"main.number_of_macro_cycles=<u></u>2" the job crashes during "MACRO_CYCLE 2 OF 2" after log-file indication<br>
" � � � � � � �----------Correcting NCS rotamer outliers----------<br>
�Set U �69 �GLU to tp10 rotamer"<br>
<br>
followed by the error message :<br>
"Traceback (most recent call last):<br>
�File "/usr/local/phenix/phenix-dev-<u></u>1391/build/intel-linux-2.6-<u></u>x86_64/../../phenix/phenix/<u></u>command_line/refine.py", line 11, in <module><br>
� �command_line.run(command_name=<u></u>"phenix.refine", args=sys.argv[1:])<br>
�File "/usr/local/phenix/phenix-dev-<u></u>1391/phenix/phenix/refinement/<u></u>command_line.py", line 161, in run<br>
� �call_back_handler=call_back_<u></u>handler)<br>
�File "/usr/local/phenix/phenix-dev-<u></u>1391/phenix/phenix/refinement/<u></u>driver.py", line 1659, in run<br>
� �ncs_manager � � � � � � = self.ncs_manager).result<br>
�File "/usr/local/phenix/phenix-dev-<u></u>1391/phenix/phenix/refinement/<u></u>strategies.py", line 170, in __init__<br>
� �ion_placement_manager = ion_placement_manager)<br>
�File "/usr/local/phenix/phenix-dev-<u></u>1391/phenix/phenix/refinement/<u></u>macro_cycle.py", line 66, in __init__<br>
� �self.call(self.ncsrot, �"NCS rotamer correction")<br>
�File "/usr/local/phenix/phenix-dev-<u></u>1391/phenix/phenix/refinement/<u></u>macro_cycle.py", line 101, in call<br>
� �func(prefix = prefix)<br>
�File "/usr/local/phenix/phenix-dev-<u></u>1391/phenix/phenix/refinement/<u></u>macro_cycle.py", line 146, in ncsrot<br>
� �log � � � � = self.log)<br>
�File "/usr/local/phenix/phenix-dev-<u></u>1391/phenix/phenix/refinement/<u></u>misc.py", line 89, in ncs_rotamer_update<br>
� �log=log)<br>
�File "/usr/local/phenix/phenix-dev-<u></u>1391/cctbx_project/mmtbx/<u></u>torsion_restraints/torsion_<u></u>ncs.py", line 1111, in fix_rotamer_outliers<br>
� �key=key)<br>
�File "/usr/local/phenix/phenix-dev-<u></u>1391/cctbx_project/mmtbx/<u></u>torsion_restraints/rotamer_<u></u>search.py", line 178, in search<br>
� �assert rotamer == cur_rotamer<br>
AssertionError"<br>
<br>
I have been using built phenix-dev-1391 (I also checked phenix version 1.8.2-1309 or built dev-1436, they crashed as well) x86_64-fc3, in �a machine running Ubuntu 10.04.4 LTS with Python 2.6.5.<br>
<br>
<br>
I tried another machine, running Ubuntu 12.04 LTS with Python 2.7.3, and using built phenix-dev-1391 x86_64-fc3 I got at the end of the log-file:<br>
" � � � � � � �----------Correcting NCS rotamer outliers----------<br>
<br>
Traceback (most recent call last):<br>
�File "/usr/local/phenix/phenix-dev-<u></u>1391/build/intel-linux-2.6/../<u></u>../phenix/phenix/command_line/<u></u>refine.py", line 11, in <module><br>
� �command_line.run(command_name=<u></u>"phenix.refine", args=sys.argv[1:])<br>
�File "/usr/local/phenix/phenix-dev-<u></u>1391/phenix/phenix/refinement/<u></u>command_line.py", line 161, in run<br>
� �call_back_handler=call_back_<u></u>handler)<br>
�File "/usr/local/phenix/phenix-dev-<u></u>1391/phenix/phenix/refinement/<u></u>driver.py", line 1659, in run<br>
� �ncs_manager � � � � � � = self.ncs_manager).result<br>
�File "/usr/local/phenix/phenix-dev-<u></u>1391/phenix/phenix/refinement/<u></u>strategies.py", line 170, in __init__<br>
� �ion_placement_manager = ion_placement_manager)<br>
�File "/usr/local/phenix/phenix-dev-<u></u>1391/phenix/phenix/refinement/<u></u>macro_cycle.py", line 66, in __init__<br>
� �self.call(self.ncsrot, �"NCS rotamer correction")<br>
�File "/usr/local/phenix/phenix-dev-<u></u>1391/phenix/phenix/refinement/<u></u>macro_cycle.py", line 101, in call<br>
� �func(prefix = prefix)<br>
�File "/usr/local/phenix/phenix-dev-<u></u>1391/phenix/phenix/refinement/<u></u>macro_cycle.py", line 146, in ncsrot<br>
� �log � � � � = self.log)<br>
�File "/usr/local/phenix/phenix-dev-<u></u>1391/phenix/phenix/refinement/<u></u>misc.py", line 89, in ncs_rotamer_update<br>
� �log=log)<br>
�File "/usr/local/phenix/phenix-dev-<u></u>1391/cctbx_project/mmtbx/<u></u>torsion_restraints/torsion_<u></u>ncs.py", line 1044, in fix_rotamer_outliers<br>
� �self.rotamer_search_manager.<u></u>prepare_map(fmodel=fmodel)<br>
�File "/usr/local/phenix/phenix-dev-<u></u>1391/cctbx_project/mmtbx/<u></u>torsion_restraints/rotamer_<u></u>search.py", line 57, in prepare_map<br>
� �torsion_utils.prepare_map(<u></u>fmodel=fmodel)<br>
�File "/usr/local/phenix/phenix-dev-<u></u>1391/cctbx_project/mmtbx/<u></u>torsion_restraints/utils.py", line 771, in prepare_map<br>
� �not exclude_free_r_reflections))<br>
�File "/usr/local/phenix/phenix-dev-<u></u>1391/cctbx_project/mmtbx/map_<u></u>tools.py", line 242, in fft_map<br>
� �symmetry_flags � �= symmetry_flags)<br>
�File "/usr/local/phenix/phenix-dev-<u></u>1391/cctbx_project/cctbx/<u></u>miller/__init__.py", line 3420, in fft_map<br>
� �f_000=f_000)<br>
�File "/usr/local/phenix/phenix-dev-<u></u>1391/cctbx_project/cctbx/<u></u>miller/__init__.py", line 4236, in __init__<br>
� �conjugate_flag=True)<br>
MemoryError"-<br>
<br>
<br>
I did not succeed to find out what may I have done wrong with the model �and/or params files<br>
Any help is highly appreciated,<br>
<br>
Carlos<br>
<br>
-- <br>
******************************<u></u>********<br>
Dr. Carlos Frazao<br>
Structural Biology Laboratory - Macromolecular Crystallography Unit<br>
ITQB-UNL, Av Republica, Apartado 127<br>
2781-901 Oeiras, P<br>
<br>
Phone: �(351)-214469666 � �FAX: � �(351)-214433644<br>
e-mail: <a href="mailto:frazao@itqb.unl.pt" target="_blank">frazao@itqb.unl.pt</a><br>
� � � �<a href="http://www.itqb.unl.pt" target="_blank">www.itqb.unl.pt</a><br>
<br>
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</blockquote></div><br></div>