On 9/6/17 1:06 PM, Ryan Ehrlich wrote: > 1.) How do I build a profile for multi-chain sequences?
You don't. These methods are designed to find single-chain templates, so one approach would be to search for templates for each chain individually, then combine all of the results into a multi-template alignment.
> 2.) I mentioned this in the first part, but I'd like to use multiple > templates for this analysis. Do I used the PDB ID and each chain > associated with the TCR, when doing so?
Not sure what you're asking here. Each template would need a unique name (align code) but you can call it whatever you want. Convention is to use PDB ID + chain ID, but you're not required to do that.
> Also how should I modify the > restraints argument between TCR chains?
What is the "restraints argument"?
> 3.) Accurate modeling of the CDR loops of the TCR (essentially the > active site) is important to my research, should I use loopmodel() or > other means for loop refinement?
This is probably a good idea.
Ben Webb, Modeller Caretaker