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