James Fethiere wrote: > I'm trying to reproduce the example for difficult modelling using the > genThreader for alignment. This part works fine, and I get a model with > ~28% id. Now, how do I get the alignment file from genthreader ready > for modeller. There is a nice example but it does not say how one gets > from html to the .ali file.

Cut and paste the alignment from the mGenThreader results into an alignment file. If you have to do this on a regular basis, you may want to write a short Perl/Python/etc. script to automate this. However, these sorts of difficult modeling cases generally require user intervention (e.g. in the tutorial case some parts of the sequence were not amenable to comparative modeling, and so were removed from the alignment).

Ben Webb, Modeller Caretaker