Molecular graphic Tools

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Molecular graphic Tools

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Outline

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

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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.

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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

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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).

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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 .

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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.

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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 .

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PDB Record Types

• Title Section
• Information of the file
• REMARK
• Primary Structure Section
• Secondary Structure Section
• Coordinate Section
• Connectivity Section

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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.

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Example
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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.

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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.

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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.

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Coordinate Section

• present the atomic coordinates.
• ATOM ?? containing the x, y, z orthogonal
  Angstrom (Å) 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.

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Example
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Connectivity Section

• CONNECT
• specify connectivity between atoms for which
  coordinates are supplied.

Example
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Comparisons

• Brief Descriptions
• Features Rankings
• Summary

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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.

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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.

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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.

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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.

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Features Rankings

• File Formats
• Portability
• Interface
• Grouping
• Display
• Modification
• Analysis
• User friendly

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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

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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

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Control Interface
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Grouping
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Grouping Example
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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

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Display Example
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Structure Mutation
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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

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