This command does a quick optimization of the structure, moving all side chains slightly to eliminate small VanderWaals’ clashes. It can also be used as a quick repair for missing side chain atoms. The minimal configuration file for Optimize is:
command=Optimize pdb=OP.pdb
It can be run from the command line:
FoldX --command=Optimize --pdb=OP.pdb
FoldX uses output-file as a tag to label different outputs from different commands in batch runs. After running Optimize you'll get two files to look at. Given output-file="TAG" the output files are:
- Optimized_TAG.pdb -> Side chain optimized model.
- OP_TAG.fxout -> energies before and after sidechain optimization
If you don't set output-file, TAG will be the pdbId of the first pdb on the batch.
