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Homology modelling applies alignment wrong

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Homology modelling applies alignment wrong

Dear all,

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. 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?

Post Situation: 
Thu, 2015-08-06 09:39

I seem to have been able to solve the problem. Apparently I had some wrong numbering in the alignment. Using the following works:


Obsioulsy(?), I have to substract 1 from the sequence number of the query...


P.S. Solved for the threaded sequence but unsolved for the state of ...

Tue, 2015-08-11 09:10