Input and output of coordinates (SOUP)

• Introduction.
• Reading/writing coordinates
  • Where are the options?
  • The set name
  • Reading coordinates from a PDB file, GETMOL
  • Reading GROMOS coordinates (GETGRO)
  • Reading C-alpha coordinates from a DSSP file with GETDSP
  • Writing coordinates in a PDB file (MAKMOL)
  • Writing coordinates in a PDB file (MAKMLR)
  • Saving the soup contents in a file (SAVSOU)
  • Restoring the soup from a file (RESSOU)
  • Saving the soup status in a file (SAVSTA)
  • Restoring the soup from a file (RESSTA)
  • Using protons
• The soup
• Looking at the contents of the soup
  • Listing the soup (SHOSOU)
  • Looking at sequence in the soup LISTR
  • Looking at the sequence in the soup LISTRR
  • Looking at atomic coordinates LISTA
  • Looking at atomic coordinates LISTAA
  • Looking for sequence patterns SHOPAT
• Cutting and pasting proteins
  • Pasting proteins (PASTE)
  • Pasting all proteins (PASTAL)
  • Cutting molecules (CUT)
  • Undoing cuts and pastes (INIPAS)
  • Listing the cut and paste flags (SHOPAS)
• Saving and restoring residues
  • Saving a residue (SAVAA)
  • Restoring saved residues (RESAA)
• Deleting, inserting, mutating, correcting, etc
  • Initialize the soup (INISOU)
  • Delete a molecule (DELMOL)
  • Delete multiple molecules (DELMLS)
  • Deleting a residue (DELETE)
  • Correcting a residue range (CORAA)
  • Correcting all residues (CORALL)
  • Listing bad residues (CNTBAD)
• Cys-cys bridge commands
  • Listing cys-cys bridges (SHOCYS)
  • Setting cys-cys bridges (SETCYS)
  • Initialization of cys-cys bridges (INICYS)
• Other soup commands
  • Adding C-terminal oxygens (ADDOXT)
  • Reading proteins from the database (GETDBF)
  • Creating a DNA molecule (MAKDNA)
  • Renumbering residues (NEWUNQ)
  • Changing or setting chain-identifiers (SETCHA)
  • Making a copy of part of the soup (SOUCOP)
• Activating more commands (MORE)
• Hidden options
  • Forcing WHAT IF to neglect errors (DVADOM)
  • Reading coordinates from a PDB file (GETUS3)
  • Looking at the pointers in the soup (STATUS)
  • Remove double molecules from the soup (CLNSOU)
  • Fixing DNA molecules (INVERT)
  • Merging drugs (MERGED)
  • Deleting complete base pairs (DELDNA)
  • Determine DNA pairing from H-bonding (HBODNA)
  • Moving molecules along the DNA (SHEARD)
  • Disabling binding junk to residues (NOBOTO)
  • Fixing DNA molecules (FIXDNA)
  • Displaying the topology file (SHOTOP)
  • Reading kinemage files (GETKIN)
  • Pasting residues (PASRNG)