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The ab initio executable is in main/source/src/apps/public/AbinitioRelax.cc. The source code for the ab initio protocol is in main/source/src/protocols/abinitio/AbrelaxApplication.cc. See the demos/abinitio directory for an example ab initio run which includes input files, expected output files, and an example run log.
InitMap is a 3D structure viewer, and by default includes the protein sequence in its appearance. If you want the protein sequence excluded from the monomer comparison, please follow the following steps.
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