Sequence design with mixed fixbb-relax protocol

This topic has 4 replies, 4 voices, and was last updated 4 years, 3 months ago by Anonymous.

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- October 3, 2013 at 3:11 pm #1665
  Anonymous
  Hello,
  
  I would like to design a protein sequence using a mixed fixbb-relax protocol.
  
  Basically, I want to do something like in this publication: http://www.sciencedirect.com/science/article/pii/S0969212612001517
  
  (The idea is to iterate between fixbb and relax protocols as long as the Rosetta energy difference between models is bigger than 1.0 REU)
  
  Does anybody have an idea how to use RosettaScripts to implement this?
  I understand that my script(below) runs fixbb, takes the best trajectory and inputs it into relax and I get output model that has gone through fixbb and relax only once. But I would like more cycles to occur and each time energy difference between cycle i and i-1 should be calculated to determine if next cycle should be made.
  
  I attach what I have done so far, XML file (as txt attachment, no other way), command and flags:
  
  ~/rosetta3.5/rosetta_scripts.
  default.linuxgccrelease @flags_designrelax -out:file:silent results.out -parser:protocol design_relax.xml
  
  -s INPUT.pdb
  -nstruct 2
  -database /mnt/db/rosetta_database3.5/
  -ex1
  -ex2
  -ndruns 3
  
  best wishes,
  Krzysiek
- October 3, 2013 at 4:20 pm #9375
  Anonymous
  So, I checked out the supplemental info, expecting a RosettaScript, and I saw a command line that involves an unreleased PilotApp.
  
  However, if you take a look at Rosetta/Demos/public/ideal_proteins, there is a mover called in the example XML flxbbdesign that iterates between relax and design. Use the example from the ideal proteins script in your XML. The reference is here:
  
  ### Principles for designing ideal protein structures ###
  ### Nobuyasu Koga, Rie Tatsumi-Koga, Gaohua Liu, Rong Xiao, Thomas B. Acton, ###
  ### Gaetano T. Montelione, and David Baker ###
  ### Nature 2012
  
  You may want to look at the packstat filter as well…
  You could use the LoopOver mover with a score filter, but I’m not exactly sure how to get exactly what you want. Maybe someone else can chime in who has more experience with RS than I do..
  
  Hope this helps at least a bit…
  
  -J
- October 8, 2013 at 3:28 pm #9388
  Anonymous
  If you do want to automate this protocol, you may want to use the IteratedConvergence mover. ( https://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/Movers_(RosettaScripts)#IteratedConvergence ) This will repeat a sub-mover (which can be a multi-step ParsedProtocol https://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/Movers_(RosettaScripts)#ParsedProtocol_.28formerly_DockDesign.29 mover) until a given filter (e.g a ScoreType filter for total_score https://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/Filters_(RosettaScripts)#ScoreType ) doesn’t change by more than a given amount. Your ParsedProtocol mover can contain both the PackRotamersMover ( Which does basically the same thing as the fixbb design https://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/Movers_(RosettaScripts)#PackRotamersMover ) and the FastRelax mover (which does basically the same thing as the relax application https://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/Movers_(RosettaScripts)#FastRelax )
- October 11, 2013 at 12:23 pm #9393
  Anonymous
  The flxbbdesign application is indeed handy, but has no documentation yet therefore it is hard to use it, but thanks for the idea.
  In the end I applied procedure proposed by rmoretti and it works great!
  
  Thank you both for help
  
  Krzysiek
- September 23, 2020 at 6:24 pm #15521
  Anonymous
  Hi,
  
  could you share the .xml file you used to apply this procedure?
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