I have been battling with a specific homology modelling for some time (I never had problems before though) and hope that you can help me further. Whichever version of homology modelling I use (3.5 and never hybrid one from the latest release), the sequence of the final model does not correspond to the sequence of the alignment I provid. It appears that a gap very early in the alignment is skipped and all following residues are hence shifted by 2 (only one more gap in ~450 res). For simplicity just the first few residues:
So, I expect the model to have the two FF/YY and following residues matching, BUT no. The first 5 match and then the sequence is shifted. Any idea what is going on here. It must be something more fundamental since when I start the alignment with the 2 aromatic residues I get the same result.
Thanks for any help, I am desperate now (after trying for several weeks),
P.S. I cannot use the robetta server since I have better exp. models available.
P.S. setup_rosettaCM.py is in an awful state. The newest does not work and the resorting to an old one required lots of patching too. Why cant there be a versio which works?