Relational protein structure database (SCAN3D)

• Introduction.
• Inspecting the database SHOENT
  • Indexing the database (DINDEX)
  • Indexing the database and parameters (SHOPAR)
  • Inspecting PDB file header (SHOHED)
  • Inspecting 3-d database sequences (SEQINF)
  • Inspecting database helix/sheet/turn determinations (SDBHST)
  • Inspecting database accessibilities (SDBACC)
  • Inspecting database torsion angles (SDBCHI)
  • Inspecting database Cys-Cys bridge administration (SDBCYS)
  • Inspecting database sequence (SDBSEQ)
  • Inspecting database sequence (SDBPRF)
  • Inspecting database sequence (SDBHBO)
  • Inspecting database sequence (SDBHMO)
• Scanning the database
  • Introduction
  • Search for sequence fragments (SEQUEN)
  • Search for secondary structure (HELSHT)
  • Search for phi-psi combinations (PSIPHI)
  • Search for omega values (OMEGA)
  • Search for conserved residues (SCNCNS)
  • Search for position in the chain (SCNPOS)
  • Search for bsckbone h-bonds (SCNHBO)
  • Search for side chain chi-angles (CHIVAL)
  • Searching for accessibility values (ACCVAL)
  • Searching sequences using Dayhoff matrix (DAYHOF)
  • Searching for turns (TURNTP)
  • Looking for hydrophobic moment values (SCNHYD)
  • Finding atomic contacts (SCNCON)
  • Finding fragments with internal contacts (NEACON)
  • Cysteines and cys-cys bridges (SCNCYS)
• Relating groups with logical operations
  • Creating groups
  • Combining groups by logical operators (SANDOR)
    • And
    • Or
    • Not
    • Xor
  • Inverting a group of hits (SCNINV)
• Evaluation of results
  • Showing groups (SHOGRP)
  • Showing hits in groups (SHOHIT)
  • Resetting the groups (INIGRP)
• Displaying hits.
  • Displaying hits one by one (SCNGRA)
  • Display all hits on top of each other (SCNGRL)
  • Display all hit environments (SCNGRN)
  • Display the environment of a hit (SCNGRE)
• Other commands
  • Changing the group length (SETLEN)
  • Defining an extra self made amino acid (SETEAA)
  • Listing the self made amino acids (SHOEAA)
  • Getting hits in the soup (SCNUSE)
  • Contact searches (DGCONT)
  • Screening with the Dayhoff matrix (DOSCAN)
  • Saving all groups (SAVGRP)
  • Restoring groups from file (RESGRP)
  • Parameters (PARAMS)
    • What to show of the hit itself (HITBBF)
    • What to show of the hits environment (HITNAF)
    • SCNCON on one residue or whole stretch (SCONTP)
    • Flag to determine where SCNGRN hits should go (HITOUT)
• Statistics on groups (SCNSTS)
  • Show for one position in a group all statistics (ONEPRF)
  • Show minimal statistics for all positions in a group (ALLPRF)
  • Show the Chi-1 statistics for one position in a group (ONECHI)
  • Show the Chi-1 statistics for all positions in a group (ALLCHI)
  • Put three dimensional Ramachandran plot in a MOL-item (GRACHI)
  • List torsion angles for residues at one position (LSTCHI)
  • Show statistics about pairs in one group (PRFPAI)
  • Bring you in the SCAN3D/SCNSTS parameter menu (PARAMS)
• Activating more commands (MORE)