Reconstructs all the side chains of a PDB. First it mutates all non-Gly residues to Ala. Then it mutates the Ala residues to the WT sequence while moving all neighbour residues with bad energies. The minimal configuration file for ReconstructSideChains is:


It can be run from the command line:

FoldX --command=ReconstructSideChains --pdb=RS.pdb

FoldX uses output-file as a tag to label different outputs from different commands in batch runs. After running SequenceDetail you'll get 2 files to look at. Given output-file="TAG" the output files are:

  • Rebuilt_TAG.pdb -> side chain repaired pdb
  • TAG_Reconstructed.fxout

If you don't set output-file, TAG will be the pdbId of the first pdb on the batch.