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