# Relax both peptide and ligands

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Relax both peptide and ligands
#1

Quick question: It is impossible with the normal Relax application to relax both the peptide chain and ligand(s), right?
Every time I have done a relax with a ligand, the ligand has not "wobbled" at all. So I currently relaxing the apostructure, add the ligand and use ligand_dock recursively for the ligands. (I know I ought to be using a tidy Rosetta script as opposed to an overly byzantine bash script that relies on a depracated application)

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Thu, 2018-09-13 03:11
matteoferla

Tell relax to sample the jump.  IDK what the flag is.  -relax:jump_move true?

Thu, 2018-09-13 15:38
smlewis
-no_jumps false

Great! In Relax? I have used it only on Remodel runs and there it is a lifesaver when stuff makes no sense. Thanks

Fri, 2018-09-14 01:30
matteoferla

It's in the relax namespace so I can only assume relax obeys it.

There is no way to know what code obeys what option other than running it and seeing if it worked (or laboriously reading the code).  You can use -show_accessed_options to determine if an option's value was ever checked, which is a partial solution.

Fri, 2018-09-14 10:34
smlewis