[modeller_usage] Modeling a sequence based on a low identity to a template

[ESTER FUSTE DOMINGUEZ <>]

Dear Sir/Madam, 
I'm trying to model a sequence based on a low identity template. 

QUESTION 1: 
I follow the example "difficult modeling" from Modeller tutorial. However, in
the last step, when I run "mod9v2 model.py" I obtain this misake described below: 
<<'import site' failed; use -v for traceback
Traceback (most recent call last):
  File "model.py", line 9, in ?
    a.make()
  File "C:\Archivos de programa\Modeller9v2\modlib\modeller\automodel\automodel
py", line 99, in make
    self.homcsr(exit_stage)
  File "C:\Archivos de programa\Modeller9v2\modlib\modeller\automodel\automodel
py", line 412, in homcsr
    self.check_alignment(aln)
  File "C:\Archivos de programa\Modeller9v2\modlib\modeller\automodel\automodel
py", line 394, in check_alignment
    aln.check()
  File "C:\Archivos de programa\Modeller9v2\modlib\modeller\alignment.py", line
182, in check
    libs=self.env.libs.modpt)
_modeller.error: read_te_291E> Sequence difference between alignment and  pdb :>>
I tried to solve it, but I could'nt. Could you help me, please?

mGenTHREADER PREDICTION RESULTS:

HTML formatted results can be found here:
http://bioinf2.cs.ucl.ac.uk/psiout/d83ffff39d5b753b.mgen.html

QUESTION 2: 

When my sequence was submitted to the mGenThreader server to fold assignment,
the server didn't returned me any significat hit, all confidence levels were
GUESS (p-value >= 0.1)
Then, which hit should I take? The hit which have the smallest p-value or the
hit with the highest percentage identity? 
Or maybe If I don't have any significat hit, all models built by MODELLER will
be wrong.Is that true?

QUESTION 3: 

In "difficult example" in MODELLER's tutorial, in this alignment, I don't know
which is the criterion to choose 30 :A: 209 :A:::: in structureX. How do you
count it? I don't undestand the way you count it. 

<<Alignment between the nsp16 sequence and the 1ej0A from mGenThreader results.

C; mGenThreader alignment of 30133975 and 1ej0A
C; CERT significance with an e-value of 1e-04
C; Percentage Identity = 14.4%
>P1;1ej0A
structureX:1ej0: 30 :A: 209 :A::::
-------GLRSRAWFKL----------------------------------DEIQQSDKLFKPGMTVVDL
GA------APGGWSQYVVTQIGGKGRIIACDLLPMDPIVGVDFLQGDFRDELVMKALLERVGDSKVQVVM
SDMAPNMSGTPAVDIPRAMYLVELALEMCRDVLAPGGSFVVKVFQGEGFDEYLREIRSLFTKVKVRKPDS
SRARSREVYIVATGRKP*

>P1;30133975
sequence:::::::::
ASQAWQPGVAMPNLYKMQRMLLEKCDLQNYGENAVIPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHF
GAGSDKGVAPG--TAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVH----------TANKWDLII
SDMYDPRTKHVTKENDSKEGFFTYLCGFIKQKLALGGSIAVKITEHS-WNADLYKLMGHFSWWTAFVTNV
NA-SSSEAFLIGANYLG*
File 30133975_1ej0A_mGenThreader.ali. Red residues were manually removed from
the alignment>>

Thank you very much. 
Ester 




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