Modeling a sequence based on a low identity to a template
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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ESTER FUSTE DOMINGUEZ wrote: > 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: ... > _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?
See the logfile for more information on the mismatch. See also http://salilab.org/modeller/FAQ.html#17
> 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?
With low quality templates, your models are likely to be incorrect.
> 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.
Actually, that's a typo - it should start from 40:A. If you look in the original PDB file, the residue numbering starts at 30 (not 1) in chain A. If you look at the REMARKS in the PDB file, they say: REMARK 999 SEQUENCE REMARK 999 RESIDUES 1-29 WERE NOT OBSERVED IN THE ELECTRON DENSITY. REMARK 999 MASS SPECTROMETRY SHOWED THAT THE PROTEIN HAD BEEN REMARK 999 PROTEOLYZED DURING CRYSTALLIZATION.
For modeling purposes we discard 10 more residues, because the alignment between these residues and the first 40 or so residues of our target sequence is so poor (thus, the model is only for part of the protein).
Ben Webb, Modeller Caretaker
participants (2)
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ESTER FUSTE DOMINGUEZ -
Modeller Caretaker