Hello all
I want to design interface of a complex which contains only alpha helices ( has not any betta strand) , it is important for me that the secondary structures of alpha helices would not be disturbed during sequence design.
Recently I have found a suitable mover '"AddHelixSequenceConstraints Mover" https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/best_practices/AddHelixSequenceConstraintsMover.
I think by using this mover during interface design some constraint in sequence design cause to preserve the secondary structure of alpha helices during design
Now I have two questions first does this mover do what I want?
and second, did I add this mover to my script in the correct place? would I add or edit something in my script ? I have attached my script here
| Attachment | Size |
|---|---|
 design raf rac 2.txt | 1.9 KB |
This mover will bias design towards sequences that favour helices at any position that is in a helix. So in that sense, yes, I think it will do what you want.
You've added it in the correct place, and have set up a scoring function correctly, but you're not passing that scoring function to the PackRotamersMover that will do the actual design. You need to change the PackRotamersMover setup to be:
<PackRotamersMover name="packrot" scorefxn="tala_comp" task_operations="design,cmdline"/>
(One other note: if you want to use the talaris2014 scoring function, which is a legacy scoring function, be sure to run Rosetta with the -restore_talaris_behavior flag. I'd recommend using the new default, ref2015, though, in which case you don't need any flags, but you do need to change talaris2014.wts to ref2015.wts.)