Hello Lisa-- > > 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
My colleague Guillermo Bermejo pointed out to be that you must be careful using actun top/par values with eefx- they are not compatible. Things may work but there are no guarantees. > rampedParams.append( StaticRamp(setupSBMFmode( pre )) ) > highTempParams.append( StaticRamp(setupSBmode( pre )) ) I think you'll want SBmode throughout, at least initially. > > --- > > 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): This is a simple bug, which is corrected in the attached version of prePotTools.py which should be placed in the python subdirectory of your Xplor-NIH 2.43 distribution. > > 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? You should include atcun.par, but all bets are off when used with eefx. You might try with standard top/par values first. best regards-- Charles
prePotTools.py
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