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I am wondering how to relax structure constraining CA in Rosetta3.2?
I found that each protocol contains two executable command such as:
is there any differences between these two?
No, it’s leftovers in the build system. The two symlinks point to the same place; the files should be identical.
I believe that the relax application is compatible with the generic constraint file flags mentioned in the constraints documentation in the manual.
You can try the flag -constrain_relax_to_start_coords.