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. A short introduction
  2. Training sections
  3. Additional resources
Example of Threaded sequence

Example of Homolgy modeling sequence

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.

1.- Short Introduction

:::::: [BACK TO MAIN]

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



    • You could very well paint it yourself (like in the old times) but obviously the only way to do it is in a computer-assisted manner.
    There are several visualization tools with a wide degree of sotisfication depending on the focus and reaching of our goals.
    A list of some avaialble tools is provided below .

    2.-TRAINING SECTIONS

    ::::::: [BACK TO MAIN] From all the available visualization tools we are going to use:
    1. Swiss-PDBViewer
    2. Protein Explorer

    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.
  • 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
    		•