Building proteins (BUILD)

• Introduction.
• Topology file
• Adding amino acids
  • Introduction
  • Start a new protein (INIBLD)
  • Extent a protein N-terminal (NBLD)
  • Extent a protein C-terminal (CBLD)
  • Grow a protein C-terminal (CBLDS)
  • Fil a gap (FILGAP)
• Building from only the sequence
  • Build from sequence file (NEWBLD)
  • Optimize cys-cys bridges (OPTCYS)
• Building in density
  • Building in density (DENFIT)
  • Building in density (DENFTS)
• Other BUILD related options
  • Parameters for the build menu (PARAMS)
    • Parameter (BLDTYP)
    • Parameter (BLDPHI)
    • Parameter (BLDPSI)
    • Parameter (BLDOME)
    • Parameter (HELIX)
    • Parameter (SHEET)
    • Moving helices through space (SETPOS)
    • Activating more commands (MORE)
• Ab initio building based on knowledge (SHAKE)
  • Reconstruct whole soup by shaking (SHAALL)
  • Model ab-initio using various constraints (SHABLD)
  • Colour ranges as function of SHAKE violation (SHACOL)
  • 'Repair' a loop using SHABLD for just a loop (SHAFIX)
  • Does multiple SHAALL runs (SHAMUL)
  • Reconstruct part of the soup by shaking (SHARNG)