On 6/15/10 2:25 PM, Thomas Evangelidis wrote: > I was looking at : > > http://www.salilab.org/modeller/manual/node26.html#SECTION:initialmodel > > and was wondering if it's right to pass a loop fragment generated de > novo into automodel with the inifile parameter.
Sure, if you like. As long as the model has the same primary sequence as your target in your alignment file, it can be any structure.
> Is it the same as using > it as a template in the alignment (that's what I do so far)? If yes, can > I define multiple infiles to model multiple loops of my protein whilst > doing homology modeling for the rest of it?
No. It merely specifies the initial (unoptimized) model. If you don't specify it, Modeller generates an initial model by threading the target sequence onto the template structure, and using internal coordinates to generate an extended chain conformation for any unaligned residues. It also differs from a template in that it has to match the sequence of your target exactly.
Ben Webb, Modeller Caretaker