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[modeller_usage] questions about multichains modeller



Dear colleagues,

I have a problem in multichain modeller. according the template file in automodel folder, I created the input file and script file. however when I run this script,  I recieved warnings listed below. Who knows how to reslove the problem? Thanks a lot!


You can find many useful example scripts in the
examples\automodel directory.
It is recommended that you use Python to run
Modeller scripts. However, if you don't have Python installed,
you can type 'mod9.12' to run them instead.

d:\Program Files (x86)\Modeller9.12>
d:\Program Files (x86)\Modeller9.12>cd examples

d:\Program Files (x86)\Modeller9.12\examples>cd automodel

d:\Program Files (x86)\Modeller9.12\examples\automodel>python model-multichain-d
ec1.py > model-multichain-dec1.log
Traceback (most recent call last):
  File "model-multichain-dec1.py", line 37, in <module>
    a.make()                           # do homology modeling
  File "d:\Program Files (x86)\Modeller9.12\modlib\modeller\automodel\automodel.
py", line 96, in make
    self.homcsr(exit_stage)
  File "d:\Program Files (x86)\Modeller9.12\modlib\modeller\automodel\automodel.
py", line 410, in homcsr
    aln = self.read_alignment()
  File "d:\Program Files (x86)\Modeller9.12\modlib\modeller\automodel\automodel.
py", line 400, in read_alignment
    aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence])
  File "d:\Program Files (x86)\Modeller9.12\modlib\modeller\alignment.py", line
78, in append
    allow_alternates)
_modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was n
ot found in the alignment file; ALIGN_CODES(       1) =  4h10

d:\Program Files (x86)\Modeller9.12\examples\automodel>