Dear Charles,
I'm refining a protein structure with PRE data of MTSL labels. There are
something wrong with my "newRefine.py" script. Followed is a part of ERROR
report.
--------------------------------------------------------
newRefine.py(164): pass
newRefine.py(162): for resid in range(777,783):
newRefine.py(169): cysp114 = PotList('cysp114')
newRefine.py(170): for (name,file,assignType) in [
newRefine.py(171): ("Cysp114hn","pre_cysp_114.tbl","normal"),
newRefine.py(173): p =
create_PREPot(name,"./inputs/"+file,assignType,500,clockResid=777)
create_PREPot: detected 1H nuclei
addClockAtoms: using existing atoms in segid: "" resid: 777
newRefine.py(174): cysp114.append(p)
newRefine.py(175): pass
newRefine.py(171): ("Cysp114hn","pre_cysp_114.tbl","normal"),
newRefine.py(176): pre.append(cysp114)
newRefine.py(179): def runSBmode():
newRefine.py(192): bbPre = PotList('bbPre')
newRefine.py(193): for p in (cysp114['Cysp114hn']):
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "/opt/xplor-nih-2.32/python/trace.py", line 180, in run
exec cmd in dict, dict
File "<string>", line 1, in <module>
File "newRefine.py", line 193, in <module>
for p in (cysp114['Cysp114hn']):
File "/opt/xplor-nih-2.32/python/potProxy.py", line 39, in __getitem__
a = getattr(o, '__getitem__')
File "/opt/xplor-nih-2.32/python/wrappers/prePot.py", line 349, in
<lambda>
realPREPot.__getattr__ = lambda self, name: _swig_getattr(self,
realPREPot, name)
File "/opt/xplor-nih-2.32/python/wrappers/prePot.py", line 54, in
_swig_getattr
raise AttributeError(name)
AttributeError: __getitem__
PyInterp::command: error executing: >execfile('newRefine.py')<
HEAP: maximum use= 3558249 current use= 3499342
-----------------------------------------------------------------------
And the below is part of my "newRefine.py" script.
-----------------------------------------------------------------------
#
# PRE restraints
#
from prePotTools import create_PREPot
pre = PotList('pre')
# add clock pseudo-atoms
#
from prePotTools import addClockAtoms
for resid in range(777,783):
addClockAtoms(resid)
pass
#
# for CYSP114
#
cysp114 = PotList('cysp114')
for (name,file,assignType) in [
("Cysp114hn","pre_cysp_114.tbl","normal"),
]:
p = create_PREPot(name,"./inputs/"+file,assignType,500,clockResid=777)
cysp114.append(p)
pass
pre.append(cysp114)
def runSBmode():
print 'configuring SB mode'
from prePotTools import setupSBmode
from simulationTools import flattenPotList
for p in flattenPotList(pre): setupSBmode(p)
#apparent tauc
tcappCysp114=3.0
for p in list(cysp114):
p.setTcType("fix")
p.setTauC( tcappCysp114 )
pass
return
bbPre = PotList('bbPre')
for p in (cysp114['Cysp114hn']):
bbPre.append(p)
pass
crossTerms.append(bbPre)
def runSBMFmode():
print 'configuring SBMF mode'
from prePotTools import setupSBMFmode
from simulationTools import flattenPotList
for p in flattenPotList(pre): setupSBMFmode(p)
pre.calcEnergy()
tcappCysp114=3.0
maxtcCysp114 = tcappCysp114 / cysp114['Cysp114hn'].aveS2()
for p in list(cysp114):
p.setTcType("opt")
p.setTauC( tcappCysp114 )
p.setTcMax( maxtcCysp114 )
pass
return
potList.append(pre)
rampedParams.append( MultRamp(0.05,1.0, "pre.setScale( VALUE )") )
rampedParams.append( StaticRamp("runSBMFmode()") )
highTempParams.append( StaticRamp("runSBmode()") )
-----------------------------------------------------------------------------------------
If I commented "bbPre = PotList('bbPre')" and followed five lines of it,
"newRefine.py" could run smoothly; but PRE restraints are not used in the
calculation.
My question is how should I set PRE parameters of "newRefine.py" or modify
input files in this case?
Thank you!
Best regards,
Yujie Wu
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