Hi,
I am designing a protein-protien interface using Rosetta Scripts, and would like to use logic in the resfile.
For example, if one amino acid at a given position is re-designed to be [list of aa], then the redesign at this other defined position should be limited to [list of aa]
Is this possible?
Also, it seems like a list of amino acids is fine to apply to one residue, but I would like to apply identical constraints to multiple residues, and it doesn't seem to like when I list residue numbers. So my file is very repetetive:
NATAA
START
334 A PIKAA NIHDGS
335 A PIKAA NIHDGS
368 A PIKAA NIHDGS
369 A PIKAA NIHDGS
402 A PIKAA NIHDGS
403 A PIKAA NIHDGS
436 A PIKAA NIHDGS
437 A PIKAA NIHDGS
470 A PIKAA NIHDGS
471 A PIKAA NIHDGS
504 A PIKAA NIHDGS
505 A PIKAA NIHDGS
538 A PIKAA NIHDGS
539 A PIKAA NIHDGS
572 A PIKAA NIHDGS
573 A PIKAA NIHDGS
606 A PIKAA NIHDGS
607 A PIKAA NIHDGS
640 A PIKAA NIHDGS
641 A PIKAA NIHDGS
674 A PIKAA NIHDGS
675 A PIKAA NIHDGS
Is it possible to condense this?
Thank you =}
This is what resfiles are supposed to look like. There is no way to make position A dependent on position B with a resfile.
There is minimal support for contiguous ranges of residues in resfiles: https://www.rosettacommons.org/docs/latest/rosetta_basics/file_types/resfiles
The most concise way to set this up, assuming you are using RosettaScripts, would be to use a ResidueSelector that listed your residues of choice, then define one TaskOperation with the effect of "PIKAA NIHDGS" - that's this one. I'm skipping some middle steps here; if you're intent on doign it, we can help, but if you already have a working resfile it's a waste of your time. (https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/TaskOperations/taskoperations_pages/Residue-Level-TaskOperations#residue-level-taskoperations_restrictabsentcanonicalaasrlt)
If you also want the DESIGNED sequences to be correlated - not chosen within NIHDGS, but also "if 200 is N, 204 is ALSO N" - there is a way to do that, too, but it's not what I think you want.