I just try to use the old waterRefineTools.py included in version 2.44 package, and it works. The cost is, water will be deleted after water refinement. Maybe something must be refined further for the new file? For the new file, I mean this one: https://nmr.cit.nih.gov/xplor-nih/updates/current/
On Mon, Feb 13, 2017 at 12:04 PM, Val Yu <[email protected]> wrote: > Hi Charles, > > Below is. They are actually the same as the one in gb1_rdc. Even after > deleting the two lines in red color, I still met the same problem. On the > other hand, the gb1_rdc wrefine.py works well in its own directory. It just > not work in my protein. > > def calcOneStructure( structData ): > from waterRefineTools import refine > protocol.initCoords(inputStructures[structData.structNum]) > refine(outFilename=structData.filename(), > potList=potList, > coolingParams=rampedParams, > keepWaters=True, > waterResname=waterResname) > pass > > > StructureLoop(numStructures=len(inputStructures), > pdbTemplate="SCRIPT_STRUCTURE.sa", > structLoopAction=calcOneStructure, > genViolationStats=True, > averagePotList=potList, > averageContext=FinalParams(rampedParams), > averageFitSel="(resid 601:640 or resid 653:752) and (name CA or name > C or name N)", > averageCompSel="(resid 601:640 or resid 653:752) and (not > resname ANI and not name H*)" > ).run() > > On Mon, Feb 13, 2017 at 8:27 AM, Charles Schwieters < > [email protected]> wrote: > >> >> >> Hello Qinhong-- >> >> > >> > I have a problem in water refinement in setting averageFitSel. Below is >> my output >> > file, showing there was something wrong. I'm sure my script worked well >> in >> > version 2.40. This problem only happens when I updated to version 2.44. >> Is there >> > any idea how can I fix it? Thanks! >> > >> > Traceback (most recent call last): >> > File "<string>", line 2, in <module> >> > File "/opt/xplor-nih-2.44/python/trace.py", line 180, in run >> > exec cmd in dict, dict >> > File "<string>", line 1, in <module> >> > File "wrefine.py", line 149, in <module> >> > averageFitSel="(resid 601:640 or resid 653:752) and (name CA or >> name C or >> > name N)", >> > File "/opt/xplor-nih-2.44/python/simulationTools.py", line 424, in >> run >> > sim.setAtomPosArr( initCoords ) >> > File "/opt/xplor-nih-2.44/python/wrappers/simulation.py", line 172, >> in >> > setAtomPosArr >> > return _simulation.Simulation_setAtomPosArr(self, *args, **kwargs) >> > SystemError: xplor-nih error: FIX: setAtomPosArr: array should have >> size numAtoms >> > PyInterp::command: error executing: >execfile('wrefine.py')< >> > >> > -- >> >> I have not been able to reproduce this issue. You might send the >> portion of your script which includes calcOneStructure and >> StructureLoop. >> >> best regards-- >> Charles >> > > > > -- > Qinhong Yu > Ames' Lab > Department of Chemistry > UC Davis > -- Qinhong Yu Ames' Lab Department of Chemistry UC Davis
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