Michael Tress
ProteinDesign Group.
Centro Nacional de Biotecnologia (C.N.B.- C.S.I.C.)
Campus Universidad Autonoma.Cantoblanco. 28049 Madrid.
Tlf: +34-91-5854570. Fax: +34-91-5854506.
Madrid-May-05

VISUALISATION TOOLS PAGE

This constitutes the last module of the practical course of protein structure. If you are here, you must have conducted some modelling or threading.

Here you will find

  1. A short introduction
  2. Training sections
  3. A Testing Visual Exercise
  4. Additional resources
Example of Threaded sequence

Example of Homolgy modelling sequence

         1.- Short Introduction

:::::: [BACK TO MAIN]


               Why do we need viewers? Well, the answer is pretty obvious. We need to "see" the real structure of a protein in order to extract useful information.
The viewers have evolved very fast. For instance 20 years ago was "blind folded" meaning: "painting it yourself". Then, the early vector graphics allow to process information from atomic coordinates. Still, the resolution was not satisfactory. Nowadays, we have programs capable of taking coordinates (most likely PDB format) and processing them to produce a graphical display output.
Features of modelling included in such tools are for example:
  • allowing changes to molecules in graphics mode
  • calculate the surfaces
  • the packing density
  • some electrostatics
  • display them graphically
  • apply force fields
  • run optimisations and minimisations
  • molecular dynamics
  • loop insertion and/or replacements
  • docking


    • HOW CAN I :
    1. visualise my model interactively?
    2. change the settings or the shape of my model?
    3. generate a nice graphical output of my model?

  • Available TOOLS
  • DEEP_VIEWER / Swiss-PDViewer
  • RASMOL/ Protein Explorer
    • Is it then possible to:
    1. Compare my model with the template?
    2. Perform an structural alignment?
    3. Trace conserved positions in a structural alignment?
  • Available TOOLs
  • GO to CE
  • GO to CONSURF

    •                               List of common viewers

    PURE VISUALISATIONVISUALISATION & MODELING
    Graphical User Interface
  • RasMol
  • CHIME (browser plug-in)
  • VRML (browser plug-in)
  • Cn3D
    		• Graphical User Interface
  • SPDBV
  • INSIGHT
  • Bragi
  • HEX
    • Script-based
  • MolMol / MolsScript
  • Dino
  • VISP
  • SETOR
    		• Script-based
  • PyMol

    •                               Nice TOOL for RENDERING

  • POV-RAY
  • POV-Ray Tutorial with DINO tool.
    • :::::: [BACK TO MAIN]



             2.- Training sections

    		:::::: [BACKTO MAIN]

    Tools that we are going to use:

    1.- Protein Explorer/Rasmol

    1. RASMOL tutorial: For help
    2. Go to PDB and get 1d66.pdb
    3. Find hydrophobic amino acids and color them red
    4. save this view
    5. restore previous view
    6. Play a little bit ....

    2.- SPDBV

    1. Swiss-PDBViewer Basic tutorial: For help
    2. Go to PDB structural database and retrieve target 1HEW
    3. Make a model in which lysozyme is shown only as a ribbon, colored by secondary structure, and tri-NAG is shown in normal (CPK) colors with a dotted van der Waals surface.
    4. Get a trypsin structure from PDB, find another homolog, superimpose them and create a nice graphical output of the alignment using POV-ray.

    3.- OK: what about NMR STRUCTURES?

    In this case, we have several solutions. We need to pick the most favorable!
  • Go to PDB database and search for Pyrin (Search lite)
  • Go to OLDERADO and get the best model
  • Edit the final PDB file
  • Color by secondary structure
  • Get the surface potential
  • save as Pov-ray view
  • Get a nice graphical output with white background

    • Why is the following enzyme inactive?