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
_______________________________________________
Xplor-nih mailing list
[email protected]
https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih