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Hi Louis,<br>
<br>
sorry for delayed reply - I was supposed to take this one but I was
out of email for a few days...<br>
<br>
A few suggestions:<br>
<br>
1) Try the latest PHENIX nightly build to see if this problem is
still there:<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.phenix-online.org/download/nightly_builds.cgi">http://www.phenix-online.org/download/nightly_builds.cgi</a><br>
<br>
2) If the problem persists then please send me the data and model
and the exact command that leads to the crash. I will work on it
once I have the data and I will let you know once the problem is
fixed. If I have it tomorrow morning then the chances are that you
will have a working solution by the end of the day.<br>
<br>
Pavel.<br>
<br>
<br>
On 10/20/10 12:17 PM, Louis Lazar wrote:
<blockquote
cite="mid:AANLkTinD1ozsciz12=WQi+s_9c4NKR1=jb4xW2d+EJRB@mail.gmail.com"
type="cite">
<pre style="font-family: courier new,monospace;">Hello,
Sorry for reposting, I am trying to get a better response with a more detailed subject line. I am seeing an internal error while trying to conduct joint x-ray/neutron refinement, and any help with the issue below would be greatly appreciated.
Thank you very much in advance:
================================ ADP refinement===============================
Traceback (most recent call last):
File
"/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/command_line/refine.py",
line 11, in <module>
command_line.run(command_name="phenix.refine", args=sys.argv[1:])
File
"/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/refinement/command_line.py",
line 89, in run
call_back_handler=call_back_handler)
File
"/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/refinement/driver.py",
line 1182, in run
call_back_handler = call_back_handler)
File
"/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/refinement/strategies.py",
line 735, in refinement_machine
h_params = h_params)
File
"/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/cctbx_project/mmtbx/refinement/adp_refinement.py",
line 192, in __init__
all_params = all_params)
File
"/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/cctbx_project/mmtbx/refinement/adp_refinement.py",
line 216, in refine_adp
model.set_refine_individual_adp()
File
"/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/cctbx_project/mmtbx/model.py",
line 1035, in set_refine_individual_adp
iselection = selection_iso.iselection())
RuntimeError: cctbx InternalError:
/net/anaconda/scratch1/phenix/phenix-1.6.4-486/cctbx_project/cctbx/xray/scatterer_flags.h(417):
CCTBX_ASSERT(f.use_u_iso()) failure.
This error occurs during the 2nd macro cycle of refinement using this
general command:
phenix.refine model.pdb data_xray.hkl
neutron_data.file_name=data_neutron.hkl
input.xray_data.labels=FOBSx input.neutron_data.labels=FOBSn
Thanks again.
Regards,
Louis
</pre>
<pre wrap="">
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</pre>
</blockquote>
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