Dear Charles, As I only have 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.
iter 0 violations: [120, 250, 237]
action: min potential terms: ['ANGL', 'BOND', 'IMPR']
number of IVM dof: 8991
iter 1 violations: [0, 0, 0]
newRefine.py(47): nconf = 1
newRefine.py(48): import protocol, xplor
newRefine.py(53): from potList import PotList
newRefine.py(54): potList = PotList()
newRefine.py(55): crossTerms = PotList()
newRefine.py(59): from simulationTools import MultRamp, StaticRamp,
InitialParams
newRefine.py(61): rampedParams=[]
newRefine.py(62): highTempParams=[]
newRefine.py(81): from prePotTools import create_PREPot
newRefine.py(82): pre = PotList('pre')
newRefine.py(86): from prePotTools import addClockAtoms
newRefine.py(87): for resid in range(777,783):
newRefine.py(88): addClockAtoms(resid)
X-PLOR>param @TOPPAR:axes.par end
ASSFIL: file /data1/program/xplor-nih-2.39/toppar/axes.par opened.
PARRDR>remark axes-1.0.par
PARRDR>remark molecule for anisotropy
PARRDR>
PARRDR>set message off echo off end
PARRDR> end
X-PLOR>end
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
PyInterp::command: error executing: >execfile('newRefine.py')<
HEAP: maximum use= 4064770 current use= 3534142
I've added the resid TAU (777-782) in my pdb file and attached is the
newRefine.py script.
Would you please give any suggestions to solve the problem ?
Thanks.
Best
Changdong
newRefine.py
Description: application/chimera
_______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
