MGiò wrote: > I'm trying and model a 7-helix trans-membrane receptor, as I don't like > the way MODELLER models my helices, while I highly appreciate its loop > modelling, I've been using the "model-myini.py" input script to model my > receptor starting from a initial.pdb containing the 7 helices already > modelled. Every MODELLER run ends with the "nselat__596E> Atom index is > out of range" error. Considering that this error changes the couple of > atoms referring to any time I delete the corresponding residue in order > to by-pass the error. I've attached to the mail the input files I used > and the log file. Can you help me?
You forgot to include your alignment file, so I can't reproduce your problem, but it may be related to a bug we fixed in the recent Modeller 8v2 release. Please try your script again with Modeller 8v2, and if the problem remains, send me your input files (with the alignment!) and I'll take a look.
Ben Webb, Modeller Caretaker