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 =
AvePot(create_PREPot("PRE","atcun.tbl","normal",eSpinQuantumNumber=1.5,paraCenter="resid
300",esim=esim.member().subSim()))
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
s.structLoopAction(s)
File "ensemble-atcun.py", line 384, in calcOneStructure
loopInfo.writeStructure(potList)
File "/xplor-nih-2.43/python/simulationTools.py", line 996, in writeStructure
makeBackup)
File "/xplor-nih-2.43/python/simulationTools.py", line 1057, in writeStructure
analyzeFilename)
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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