Using logic in resfile, Rosetta Scripts

[Anonymous]

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 =}

[Anonymous]

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.

[Anonymous]

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.

[Anonymous]

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.

[Author]

Posts