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Molecular graphic Tools

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Title: Molecular graphic Tools


1
Molecular graphic Tools
  • B92902080???B92902082???B92902086???B92902107??
    ?

2
Outline
  • History of Visualization of Biological
    Macromolecules in computer representations.
  • Common feature of molecular view display software
  • PDB file format
  • Demo
  • Software comparition
  • Conclusion

3
History
  • 60 70 -Carroll K. Johnson, released ORTEP,
    a program to produce stereoscopic drawings of
    molecular and crystal structures.-In the mid
    1970's, a protein structure was solved
    crystallographically and visualized entirely with
    computers for the first time by David and Jane
    Richardson and colleagues.-In 1977 a wireframe
    Atlas of Macromolecular Structure was published.
    -Also in the late 1970's, Thomas K. Porter then
    of the Division of Computer Research and
    Technology (DCRT), NIH developed computer
    algorithms for shaded spacefilled
    representations.

4
History
  • TAMS Teaching Aids for Macromolecular Structure,
    1980 use stereo image put in two two
    conventional slides with polarizing
    filters.Image fromhttp//www.umass.edu/microb
    io/rasmol/history.htm

5
History
  • computer system for crystallographers
    manufactured by Evans Sutherland, displayed the
    electron density map, and enabled an amino acid
    sequence to be fitted manually into the map. The
    color display showed a wireframe rendering of the
    amino acid chain, and could be rotated in real
    time. These systems used scalable vector
    graphics. Rapid rotation was accomplished with
    three hardware matrix multipliers (one for each
    dimension, X, Y, and Z).

6
History
  • Kinemage (kinetic image) 1992A computer graphic
    representation of molecular structure described
    by David and Jane Richardson with supporting
    program MAGE ,PREKIN.By virtue of its
    implementation on the Macintosh, this was the
    first molecular visualization program .

7
History
  • RasMol, 1993 A free software for looking at
    macromolecular structure and its relation to
    function which is develop by Roger Sayle.
  • Chime, 1996 The development of Chime is leaded
    by Bryan van Vliet and Tim Maffett at MDL
    Information Systems, Inc. It uses an adaptation
    of the rendering and command-language from
    RasMol.

8
Common features
  • File input most of them accept .pdb file.
  • Display rotate structure, zoom in zoom out.
  • Rendering by ribbon, sticks, ballsticks, CPK,
    points, trace, cartoons, etc.
  • Color the structure atoms, H bonds, secondary
    structure, etc.
  • Clipping set clipping size .

9
PDB Record Types
  • Title Section
  • Information of the file
  • REMARK
  • Primary Structure Section
  • Secondary Structure Section
  • Coordinate Section
  • Connectivity Section

10
Information of the file
  • HEADER
  • uniquely identifies a PDB entry through the
    idCode field.
  • TITLE
  • a title for the experiment or analysis that is
    represented in the entry.
  • COMPND
  • describes the macromolecular contents of an
    entry.
  • SOURCE
  • specifies the biological and/or chemical source
    of each biological molecule in the entry.
  • KEYWDS
  • contains a set of terms relevant to the entry.
  • EXPDTA
  • identifies the experimental technique used.
  • AUTHOR
  • the names of the people responsible for the
    contents of the entry.

11
Example
12
REMARK
  • present experimental details, annotations,
    comments, and information not included in other
    records.
  • REMARK 1 ?? lists important publications related
    to the structure presented in the entry.
  • REMARK 2 ?? states the highest resolution, in
    Angstroms, that was used in building the model.
  • REMARK 3 ?? presents information on refinement
    program(s) used and the related statistics.
  • REMARK 4 999 ?? consist of free text
    annotation, predefined boilerplate remarks, and
    token value pair styled templates.

13
Primary Structure Section
  • DBREF
  • provides cross-reference links between PDB
    sequences and the corresponding database entry or
    entries.
  • SEQADV
  • identifies conflicts between sequence
    information in the ATOM records of the PDB entry
    and the sequence database entry given on DBREF.
  • SEQRES
  • contain the amino acid or nucleic acid sequence
    of residues in each chain of the macromolecule
    that was studied.
  • MODRES
  • provides descriptions of modifications (e.g.,
    chemical or post-translational) to protein and
    nucleic acid residues.

14
Secondary Structure Section
  • HELIX
  • used to identify the position of helices in the
    molecule.
  • SHEET
  • used to identify the position of sheets in the
    molecule.
  • TURN
  • identify turns and other short loop turns which
    normally connect other secondary structure
    segments.

15
Coordinate Section
  • present the atomic coordinates.
  • ATOM ?? containing the x, y, z orthogonal
    Angstrom (Ã…) coordinates for atoms in standard
    residues (amino acids and nucleic acids).
  • HETATM ?? for atoms in nonstandard residues
    (include inhibitors, cofactors, ions, and
    solvent).
  • TER ?? indicates the end of a list of ATOM/HETATM
    records for a chain.

16
(No Transcript)
17
Example
18
Connectivity Section
  • CONNECT
  • specify connectivity between atoms for which
    coordinates are supplied.

Example
19
Comparisons
  • Brief Descriptions
  • Features Rankings
  • Summary

20
Brief Descriptions (1/4)
  • BioEditor
  • A tool to collect bioinfos into a single file,
    including molecular view, sequence, reference,
    with a built-in browser.
  • Chimera
  • A highly extensible tool developed by UCSF, for
    providing a interactive molecular visualizing
    way.

21
Brief Descriptions (2/4)
  • KiNG
  • A software for displaying kinemage file,
    operating as a Java applet to promote easy access
    to kinemages from a web browser.
  • QMol
  • A OpenGL based molecular for molecular surface
    rendering, with user defined colors, transparency
    and surface-only clipping.

22
Brief Descriptions (3/4)
  • RasMol
  • A molecular view displaying program, giving a
    tiny but easy environment.
  • Swiss-PDB Viewer (SPDV)
  • A program presented by Swiss Institute of
    Bioinformatics for not only viewing but building
    models, with complex computing tools.

23
Brief Descriptions (4/4)
  • Chime
  • A browser plug-in developed by RasMol, for being
    integrated with HTML.
  • PyMol
  • A open software written in python, with
    extensions models.

24
Features Rankings
  • File Formats
  • Portability
  • Interface
  • Grouping
  • Display
  • Modification
  • Analysis
  • User friendly

25
File Formats
  • Import file type
  • PDB
  • kingmage KiNG
  • Export image
  • bmp, png, jpg
  • Chime cant export image
  • Export model file
  • PDB
  • Session Chimera, Chime, SPDV, PyMol
  • Animation
  • Chimera real time
  • SPDV png
  • PyMol Model movie
  • Others play frame

26
Portability
  • Browser plug-in
  • BioEditor Chime
  • Installation required
  • Not necessary for QMol, RasMol, SPDV
  • Platform
  • Windows, Mac, Linux
  • Mac except QMol
  • Linux except Chime
  • XWindow QMol

27
Control Interface
28
Grouping
29
Grouping Example
30
Display
  • Show/hide
  • by selected groups
  • QMol cant hide groups
  • Side chain backbone
  • switch separately
  • Rendering
  • ribbon, ball, stick, sphere
  • Labels
  • atom, AA, groups
  • KiNG can draw labels
  • Color
  • by selected groups
  • default color settings
  • CPK, B-factor, structure

31
Display Example
32
Structure Mutation
33
Analysis
  • Atoms
  • angle, dihedral angle, surface area
  • QMol can only measure surface area
  • Bonds
  • H bond, bond length, torsion
  • SPDV provides Ramachandram plot
  • Whole model
  • energy, electrostatic, alignment, superimposing

34
Analysis Example
35
User Friendly vs. Functionality
36
  • Thanks for your attention.
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