Hello Changdong--
> >>
> >> I'm using xplor-nih-v2.39 to calculate protein-dna structures based on
> >> PRE and NOE data . There are something wrong with my "newRefine.py"
> >> script. Followed is the ERROR report.
> >>
> >> addClockAtoms: using existing atoms in segid: "" resid: 777
> >> Traceback (most recent call last):
> >> File "<string>", line 2, in <module>
> >> File "/data1/program/xplor-nih-2.39/python/trace.py", line 180, in run
> >> exec cmd in dict, dict
> >> File "<string>", line 1, in <module>
> >> File "newRefine.py", line 88, in <module>
> >> addClockAtoms(resid)
> >> File "/data1/program/xplor-nih-2.39/python/prePotTools.py", line 313,
> >> in
> >> addClockAtoms
> >> oAtom = AtomSel(resSel + " and name "+oname )[0]
> >> File "/data1/program/xplor-nih-2.39/python/wrappers/atomSel.py", line
> >> 97, in __getitem__
> >> def __getitem__(self, *args, **kwargs): return
> >> _atomSel.AtomSel___getitem__(self, *args, **kwargs)
> >> IndexError: PyConvert error: range error
> >>
> >> I've added the resid TAU (777-782) in my pdb file and attached is the
> >> newRefine.py script.
> >>
> >
> > Your clock atoms probably have different naming than what is
> > expected. I suggest you delete your clock atoms and try again.
> >
>
>
> Yes, the script works after the clock atoms were deleted (xplor-nih
> version 2.39).
>
> Another question is that the correlation times are optimized and
> the tauc values are encoded using clock atoms in the newRefine.py. If the
> clock atoms were deleted, the optimized procedure will not be executed and
> the value was fixed without the clock atoms, right? In other words, the
> optimized procedure is not necessary?
The function addClockAtoms adds the clock pseudoatoms, and then the
initial value of tauc is the value you specify in the script, but it
is later optimized. The PRE setup in the newRefine.py script is much
more complicated than you need for the current situation. The whole
setup, including clock atom setup (lines 81-167 in the script you
sent) can be replaced by the snippet below. In this case tauc will
vary in the range 6.5..26 ns.
best regards--
Charles
from prePotTools import create_PREPot
pre = PotList('pre')
for (name,file,assignType) in [
("Es4hn800","preG2hn800.tbl","normal"),]:
p = create_PREPot(name,"inputs/"+file,assignType,800,tauc=13.0)
pre.append(p)
pass
potList.append(pre)
rampedParams.append( MultRamp(0.05,1.0, "pre.setScale( VALUE )") )
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