Dear Thomas!
It is hard to tell which of the examples you used as a template for the top file, but I can imagine two possibilities: either you are using your alignment as it is or you perform automatic alignment after reading it. In both cases it is possible that you won't be happy with the alignment. Then the only solution is to edit the alignment manually or to use other software to align or to play with the parameters of the alignment routine (ALIGN2D).
The most simple and easy solution is the first one, I guess...
Happy landings!
Azat.
Thomas Blicher wrote: > > Dear Modellers. > > I am trying to model MHC class I molecules and have come across a > problem which appears to be related to the alignment. MHC molecules > consist of three individual peptide chains and I have therefore > specified my input sequence in the alignment file with the chain break > character / (see alignment file below). > When modelled, this gives rise to a model with a serious flaw: It > appears that the chain break character is interpreted by MODELLER as a > kind of "dummy residue". The result is that the first chain is > modelled nicely, but the second and third chains are shifted by one > and two residues, respectively. This is a BIG problem, especially as I > am interested in the exact interactions of the third chain (a small > oligopeptide) with the rest of the molecule. > I have come up with a temporary "solution" (hopefully) where I simply > delete the last residue of the first and second chain in order to make > room for the "dummy residue". This produces nice models (which are > lacking two residues), but I would like to be able to model the entire > molecule. > > This is my alignment file which is modelled by the model.top routine: > > > >P1;1hhi > structureX:1hhi: 1:A : 9:C : MHC I: HLA-A0201: > * > >P1;1A11 > sequence:1A11: 1:A : @:@ : MHC I: HLA-A1101: > GSHSMRYFYTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAP > WIEQEGPEYWDQETRNVKAQSQTDRVDLGTLRGYYNQSEDGSHTIQIMYG > CDVGPDGRFLRGYRQDAYDGKDYIALNEDLRSWTAADMAAQITKRKWEAA > HAAEQQRAYLEGRCVEWLRRYLENGKETLQRTDPPKTHMTHHPISDHEAT > LRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVP > SGEEQRYTCHVQHEGLPKPLTLRWE/ > MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKV > EHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM > /GILGFVFTK > > * > > I've probably forgotten something essential, but I don't see what it > is. I would be happy for any comments and suggestions. > > Many thanks. > > Thomas > > > --------------------------------------------------------------------------- > Thomas Blicher, Department of Chemistry, > Universitetsparken 5, Copenhagen University, 2100 Copenhagen Denmark. > phone: 45-35320280, fax: 45-35320299 > E-mail: thomas@kage.ki.ku.dk > >