Using FiltRest3D from the command line

To rank a set of decoys you can use a web interface or install the program on your own workstation. The models to be scored can be given in Protein Databank file format, Rosetta silent file format or CABS' trajectory format.

Restraint file syntax

General restraint file syntax is:

// Comment
DEFAULT_WEIGHT <- 1.0

RESTRAINT_TYPE_NAME (
  RESTRAINT_DECLARATION
  RESTRAINT_DECLARATION
  ...
)

There are following restraint types (restraint type name in parentheses):

Distance restraints

If we want to have C-alpha at least 4.5 Angstroms apart and C-beta atoms within at most 7.3 Angstroms distance:
dist (
   (V10)-(D34) (CA>4.5  CB<=7.3)
)
To restraint SG atom of the residue C140 to be within 4 angstroms from OE1 atom of residue E33:
dist (
   C140_near_E33: (C140)-(E33) (SG-#OE1#<=4)
   )

Secondary structure assignment and percentage composition

Secondary structure can be assigned to segments using helix, strand and coil declarations.

helix ( 
   h1: 90-112
   h2: 175-193
)

strand (
   s1: 12-21   
   s2: 34-43
)

coil ( c1: 201-205 )

Secondary structure percentage in the overall structure composition can be described in the ss_composition block:

ss_composition (
  20 < helix  < 50
  15 < strand < 40
)

Above code declares between 20% to 50% of aminoacids in helices, and between 15% to 40% of aminoacids in beta strands.

Solvent accessibility

The example below declares unnamed aminoacid 45th as having between 40% to 90% accessibility, Glycine 56th as having 30% to 60% accessibility, and alanine 20th as having between 80% to 90% accessibility.
access (
       45 40-90
       Gly56 30-60
       A20 80-90 weight<-1.5
)

Protein shape fit

'Situs' or '3SOM' strings select the name of electron density matching program, and the last string defines file name. Appropriate surface shape will be converted into electron density first, using pdblur program from Situs. [Installation process is described here.]

edm (
  surface1: 'Situs' 'saxs_data.pdb'
)

edm (
  surface2: '3SOM' 'remote_model_with_filler_atoms.pdb'
)

Conjunction and alternative

To declare composite restraint having score of minimum or maximum of two other restraints, the following restraint blocks can be used:
and (
  access (
       Gly56 30-60
         )
  access (
       Glu45 40-90
         )
)

Restraint weights

Default restraint weight is 1.0, but it can be changed:
DEFAULT_WEIGHT <- 2 
dist (
   (V10)-(34-36) (CA<4.5 weight<-2 // C-alpha penalty will be multiplied by 2.0
                  CB<=7.3 weight<-1.5) // C-beta penalty will be multiplied by 1.5
)

Restraint weight selection

Careful choice of restraint weights is the most important part after restraint selection. The suggested procedure is:
The downside of skyline.py is that the found weights should be manually assessed for their plausibility and the structures can be less reliably picked. The upside is that you may get the definitive answer that the set of restraints is inadequate independently of choosen weights, or you may see what features of the protein are harder to model.
The rules of a thumb for restraint weight selection is:
restraint typerestraint type tokenweight multiplier
for fuzzy distance restraints between long segmentsdist4.0-8.0
lots of alternativesor4.0
secondary structure segmentsstrand
helix
coil
flexible
4.0
for aminoacid-aminoacid or atom-atom distance restraintsdist1.0
aminoacid accessibilityaccess0.5
maximum penalty of many restraintsand0.5
othersedmnot enough data collected
Copyright '2006 by Michal J. Gajda