I just saw there's an update on Xplor-NIH website and it's just fixing this keepwater problem. No problem now!
On Wed, Feb 8, 2017 at 10:39 PM, Val Yu <[email protected]> wrote: > Hi there, > > I use the wrefine.py script provided in xplor-NIH tutorial and set > keepwaters = true. The script looks like this: > > ...... > > from simulationTools import StructureLoop > > 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() > > > During calculation, I found water was really kept in structures. However, > when calculation was done, water was removed from all structures. How can I > stop this? > > -- > Qinhong Yu > Ames' Lab > Department of Chemistry > UC Davis > -- Qinhong Yu Ames' Lab Department of Chemistry UC Davis
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