I'm attempting to refine a structure against ATCUN PRE R2 relaxation data, but 
am hitting some errors. 

We've successfully added the ATCUN motif to the protein using the 
eginput/PSF_generation/tags/atcun_motif/addATCUN.py script

We've modified an ensemble script (with eefx now working, thank you), starting 
from the newly generated ATCUN-protein.pdb and adding the prePot potential


from prePotTools import create_PREPot,setupSBmode,setupSBMFmode
pre = 
potList.append( pre )
rampedParams.append( MultRamp(0.05,1.0, "pre.setScale( VALUE )") )

#have also tried using the SBmode things - though it looks like that was to 
combine multiple PRE data sets and we have only one:
rampedParams.append( StaticRamp(setupSBMFmode( pre )) )
highTempParams.append( StaticRamp(setupSBmode( pre )) )


This will run fine (if not doing a great job satisfying the PRE data), but is 
giving an error during writeStructure:
"Error calculating structure 0: 'PREPot' object has no attribute '__getitem__'
Warning: fitting EnsembleSimulation structures"

The bottom of the output file:

ensemble-atcun.py(384):     loopInfo.writeStructure(potList)
Traceback (most recent call last):
  File "/xplor-nih-2.43/python/simulationTools.py", line 465, in run
  File "ensemble-atcun.py", line 384, in calcOneStructure
  File "/xplor-nih-2.43/python/simulationTools.py", line 996, in writeStructure
  File "/xplor-nih-2.43/python/simulationTools.py", line 1057, in writeStructure
  File "/xplor-nih-2.43/python/simulationTools.py", line 2401, in analyze
    tmp = analyzeFunc(list(potList)+list(extraTerms))
  File "/xplor-nih-2.43/python/prePotTools.py", line 693, in analyze
    (name , pre.rms(), Qfactor(pre), pre.tc()*1e9, pre.violations())
  File "/xplor-nih-2.43/python/prePotTools.py", line 216, in Qfactor
    prelist = flattenPotList(term)
  File "/xplor-nih-2.43/python/simulationTools.py", line 2240, in flattenPotList
    for pot in potList:
  File "/xplor-nih-2.43/python/potProxy.py", line 40, in __getitem__
    return a(index)
  File "/xplor-nih-2.43/python/potProxy.py", line 39, in __getitem__
    a = getattr(o, '__getitem__')
AttributeError: 'PREPot' object has no attribute '__getitem__'


So - do we need to explicitly include the atcun.par file in our refine runs as 
is done int he addATCUN.py? Or is the error coming from something else? 

Thanks for any input you have. Haven't had any luck finding an example xplor 
script that refines against ATCUN data in particular. And I tend to complicate 
things further always wanting to run as an ensemble!

Lisa Tuttle
Klevit lab
University of Washington

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