Saravanan wrote: > I am modeling a protein in which two subunits are linked by a "propep" > which is not present in crystal structurei.e, its cleaved when protein > is active. I want to generate models without the "PROPEP". > > Crystal Structure available looks like this: (chain a and b) > > aaaaaaaaaabbbbbbbbbbb > > Model sequence is like this : (chain a and b and p-propep) > > aaaaaaaaaaapppppppppppppppbbbbbbbbbbb > > Model structure should be like this : (chain a and b AND propep chain p > should not present) > > aaaaaaaaaaabbbbbbbbbbb

I don't think I fully understand your question, because the model structure always has the same sequence as the "model sequence", by definition. If you don't want to have the propep sequence in your model, just don't include it in the model sequence in your alignment. If, on the other hand, you want to build a model containing the propep sequence but you don't want to write it into the output PDB file, you can either edit the output PDB file by hand, or you can use selection() to select the non-propep parts and then selection.write() to write out a PDB.

Ben Webb, Modeller Caretaker