SequenceDetail

It prints the sequence information of the protein in a column format: AA, Chain, Pdb Number. The minimal configuration file for SequenceDetail:

command=SequenceDetail
pdb=SD.pdb

It can be run from the command line:

FoldX --command=SequenceDetail --pdb=SD.pdb

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

  • SD_TAG.fxout -> sequence information If you don't set output-file

TAG will be the pdbId of the first pdb on the batch.

SequenceDetail energy terms

This is the field description of the output file for the output SD_TAG.fxout in the same order they appear on the file.

Title energy_description
Pdb Pdb file
three_letter Three letter residue code
chain Peptide chain of the residue
pdb_seq_num residue number in pdb
omega Ω angle
phi Ø angle
psi ψ angle
sec_struct DSSP information
total Residue contribution to the total energy
backHbond Backbone Hbond contribution
sideHbond Side chain Hbond contribution
energy_VdW Contribution of the VanderWaals
electro Electrostatic interactions contribution
energy_SolvP Penalization for burying polar groups
energy_SolvH Contribution of hydrophobic groups
energy_vdwclash Penalization due to VanderWaals’ clashes
entrop_sc Entropy cost of fixing the side chain
entrop_mc Entropy cost of fixing the main chain
sloop_entropy ONLY FOR ADVANCED USERS
mloop_entropy ONLY FOR ADVANCED USERS
cis_bond Cost of having a cis peptide bond
energy_torsion Contribution to VanderWaals’ torsional clashes
backbone_vdwclash Backbone-backbone VanderWaals. These are not considered in the total
energy_dipole Electrostatic contribution to the helix dipole
water Residue contribution of water bridges
disulfide Residue contribution of disulfide bridges
energy_kon Contribution to electrostatic interaction between molecules in the precomplex
partcov Interactions with bound metals
energyIonisation Contribution to ionisation energy
entr_complex Residue contribution to entropy cost of forming a complex
Hetero Backbone HBond total energy of the backbone of that residue with heteroatoms
Hetero Sidechain Hbond total energy of the sidechain of that residue with heteroatoms
Sidechain Accessibility total sidechain residue volumetric accessibility
Mainchain Accessibility total main chain residue volumetric accessibility
Sidechain Contact Ratio Sidechain Contact Ratio
Mainchain Contact Ratio Mainchain Contact Ratio
ab_index *