Hello Qinhong-- > > 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? >
I have reproduced the behavior you describe. I have an updated version of waterRefineTools on the web site at https://nmr.cit.nih.gov/xplor-nih/updates/current/ If you copy this updated file to the python subdirectory of the Xplor-NIH distribution, waters should be present if you rerun the calculation. best regards-- Charles _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
