Ana Rojas Mendoza.
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.
e-mail: arojas@gredos.cnb.uam.es
Madrid-Feb-04

VISUALIZATION TOOLS PAGE

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

Here you will find

  1. The course presentation
  2. A short introduction
  3. Training sections
  4. Additional resources
Example of Threaded sequence

Example of Homolgy modeling sequence

         1.- Short Introduction

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               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 to take coordinates (most likely PDB format) and process those to produce a graphical display output.
Features of modeling 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 replacementes
  • docking
  • And more things....


    •                               What can I do with my models?

                                         Now, WHAT COMES NEXT?


    HOW CAN I :
    1. visualize 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 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 VISUALIZATIONVISUALIZATION & 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.
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             2.- Training sections

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    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 aminoacids 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 MRN 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
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             3.- ADDITIONAL RESOURCES

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    VISUALIZATION TOOLS

    Molecular Graphics/ Visualization tools
  • RASMOL
    		• GENERAL TOOL for visualizing structures. Linux
  • PROTEIN-EXPLORER
    		• An IMPROVED RASMOL VERSION FOR WINDOWS-NEEDS CHIME.
  • DEEP-VIEWER
    		• A nice visualization tool.
  • GRASP
    		• Partiularely useful for the display and manipulation of the surfaces of molecules and their electrostatic properties (SGI ONLY)
  • BRAGI
    		• Very cool tool (LINUX, SGI ONLY)
  • O
    		• O is a general purpose macromolecular modelling environment.
  • BobScript
    		•  This manual describes Robert Esnouf's extensions to version 1.4 of MolScript..
  • CONSCRIPT
    		•  a programm for generating electron density isosurfaces
  • ENDscript
    		•  ENDscript is an interface grouping eight types of programs:
    1. BLAST
    2. MULTALIN
    3. CLUSTALW
    4. DSSP
    5. CNS
    6. ESPript
    7. BOBSCRIPT/ MOLSCRIPT
    8. PHYLODENDRON
    9. PROFIT.
    It aims to produce from a single PDB file four PostScript figures containing most required sequence and structure information on a protein of known structure. .
  • ESPrip
    		•  ESPript, Easy Sequencing in Postscript, is a utility to generate a pretty PostScript output from aligned sequences.
  • GRASP
    		•  GRASP is a molecular visualization and analysis program. It is particularly useful for the display and manipulation of the surfaces of molecules and their electrostatic properties.
  • MolMol
    		•  MOLMOL is a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with special emphasis on the study of protein or DNA structures determined by NMR. The program runs on UNIX and Windows NT/95/98/2000 and is freely available.
  • Molscript
    		• MolScript is a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations.
  • MolSof
    		• Commercial charge.
  • Povscript+
    		•  This website is designed to illustrate and explain the potential uses of povscript+, a modified version of molscript (Per Kraulis) and its complementary povray patch povscript (Dan Peisach) - thus povscript+.
  • Pov4Grasp
    		• a patch version of POV-ray with direct support for GRASP surfaces
  • QUE
    		• "Que" is a program for the macromolecular structure visualization on the Windows platform
  • Rarter3D
    		•  Raster3D is a set of tools for generating high quality raster images of proteins or other molecules.
  • Spock
    		•  Spock has the features users have come to expect from molecular graphics software including several bond and atom rendering types, and a complete array of backbone "worm" representations. Further, spock can calculate and display molecular and accessible surfaces, and color code these surfaces by properties (such as electrostatic potential).
  • MAIN
    		•  MAIN is an interactively driven computer program dealing with computational parts of macromolecular crystallography in progressively automated manner.
  • Turbo-Frodo
    		•  The Web Page Designed for Turbo Frodo and Turbo X Users Turbo Frodo is a general purpose molecular modelling environnement aimed at people with the needto model de novo macromolecules, polypeptides as well as nucleic acids.
  • XtalVIEW
    		•  XtalView is a crystallographic software package for fitting electron density maps and solving structures by MIR and MAD.


    STRUCTURE ANALYSIS
    cation-pi interaction analysis
  • castP
    		•  A Server for Identification of Protein Pockets & Cavities
  • ConSurf server
    		•  identification of functional regions in proteins
  • DALI
    		•
  • Evolutionary Trace Server

  • Indonesia
    		• integrated program package for biological sequence analysis. Includes Structure-based multiple sequence alignment.
  • LigPlot
    		•  schematic diagrams of protein-ligand interactions.
  • MolProbity
    		•
  • PARVATI
    		• Protein Anisotropic Refinement Validation and Analysis
  • PINTS
    		•  Patterns in Non-homologous Tertiary Structure
  • PRODRG Server-Dundee
    		•
  • Protein-Protein Interaction Server
    		•
  • SSBOND
    		•  Model building of disulfide bonds (Bart Hazes)
  • Stralign
    		•  Structure alignment for 3D protein structures.
  • SURFNET
    		•  Surfaces, cavities, etc.
  • TOPS
    		• protein topology cartoons (EBI)
  • Uppsala Software Factory
    		•  (USF).

    SELF-TEACHING
    Solving an MIR structure
  • Kevin Cowtan's homepage
    		•
  • Macromolecular Crystallography Web Server
    		•
  • Mike Sawaya Crystallographic Tutorials
    		•
  • (IUCr) Teaching Pamphlets
    		•
  • Phase Determination by Isomorphous Replacement
    		•
  • X-tal protocols
    		•

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