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
------------------------------------------------- This mail sent through IMP: http://horde.org/imp/