aria-discuss - [aria-discuss] Fwd: Next step in calculations

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[aria-discuss] Fwd: Next step in calculations

From: "Kelly, Mark" <Mark.Kelly AT ucsf.edu>
To: Benjamin Bardiaux <bardiaux AT pasteur.fr>, "aria-discuss AT services.cnrs.fr" <aria-discuss AT services.cnrs.fr>
Cc: "Longbotham, James" <James.Longbotham AT ucsf.edu>
Subject: [aria-discuss] Fwd: Next step in calculations
Date: Wed, 29 Apr 2020 17:50:04 +0000
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Hello All,

we tried to restart a run that had been successful before and get the error below - would anyone have a suggestion what might be wrong?

hope all are safe and well,

Mark

Begin forwarded message:

From: "Longbotham, James" <James.Longbotham AT ucsf.edu>

Subject: RE: Next step in calculations

Date: April 29, 2020 at 10:37:57 AM PDT

To: "Kelly, Mark" <Mark.Kelly AT ucsf.edu>

Ok so that last run I described below failed. I thought it ould have something to do with the merged restraint lists so I tried to run it again with the restraints I used previously (before assignment) and it failed still! See error below. Not sure what’s going on

Exception in thread Thread-1:

Traceback (most recent call last):

File "/programs/x86_64-linux/ccpnmr/2.4.2/python2.7/lib/python2.7/threading.py", line 810, in __bootstrap_inner

    self.run()

File "/programs/x86_64-linux/aria/2.3.1/src/py/aria/JobManager.py", line 193, in run

    f(self)

File "/programs/x86_64-linux/aria/2.3.1/src/py/aria/JobManager.py", line 331, in job_done

    self.dispatch_job(host)

File "/programs/x86_64-linux/aria/2.3.1/src/py/aria/JobManager.py", line 337, in dispatch_job

    self.done()

File "/programs/x86_64-linux/aria/2.3.1/src/py/aria/JobManager.py", line 384, in done

    self.__callback()

File "/programs/x86_64-linux/aria/2.3.1/src/py/aria/cns.py", line 2662, in <lambda>

    callback = lambda v = vars, f = self.refine_done: f(v)

File "/programs/x86_64-linux/aria/2.3.1/src/py/aria/cns.py", line 2522, in refine_done

    self.__callback()

File "/programs/x86_64-linux/aria/2.3.1/src/py/aria/Protocol.py", line 654, in <lambda>

    c = self.structure_calc_done: c(engine, molecule, it)

File "/programs/x86_64-linux/aria/2.3.1/src/py/aria/Protocol.py", line 624, in structure_calc_done

    ensemble = engine.getEnsemble(it_settings, molecule)

File "/programs/x86_64-linux/aria/2.3.1/src/py/aria/cns.py", line 666, in getEnsemble

    ensemble.read(pdbfiles, molecule, float_files = swapped_atoms)

File "/programs/x86_64-linux/aria/2.3.1/src/py/aria/StructureEnsemble.py", line 194, in read

    pdb_dict = self.reader.read(files[j], chain_types, format[j])

File "/programs/x86_64-linux/aria/2.3.1/src/py/aria/PDBReader.py", line 186, in read

   dict['noe_violations'] = float(data[13:].split(',')[0])

ValueError: could not convert string to float: D1_ApoH3_violations_1.pdb"

[aria-discuss] Fwd: Next step in calculations, Kelly, Mark, 04/29/2020

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[aria-discuss] Fwd: Next step in calculations