Bioinfo Visual

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Bioinformatics Visualization Tools
By SeLnIkRaJ
Mail me at Selnikraj@yahoo.com
SeLnIkRaJ www.selnikraj.110mb.com Visit this and Get more
QMOL
Aim
To visualize the secondary structure of a protein molecule using Qmol visualization tool.
Description
Qmol is a program for viewing molecular structures and animating molecular trajectories.
Originally based on the molview demo program by Mark Kilgard (from his book,
Programming OpenGL for the X Window System) and inspired by the Xmol program.
Qmol is similar to programs like VMD , MolMol , weblab, Swiss-Pdb Viewer,
MolScript, Rasmol, gOpenMol and ICM, but opts for fast, high quality rendering of
molecules with an easy to use user interface
It supports the following
• Wire frame, Stick figure, Ball and stick, Point, Space-

filling, Solid and Flat ribbon, Trace and Tube
• Display of multiple molecular models (as used in NMR)
• Animate molecular trajectories
• Dynamic modification of the color scheme (including
color-by-element, color-by-atom-number, color-by-
residue-number, color-by-temperature, color-by-occupancy
and New: color-by-residue-index)
Molecular
• Dynamic lighting
Display Options
• Adjust atomic radii (including radii-by-temperature and
radii-by-occupancy)
• Stereo view
• User defined clipping plane with rendered sphere/plane
intersections
• Molecular Surfaces
• New: Simultaneously view and independently manipulate
an arbitrary number of molecules.
• New: Superimpose two molecules (by rigid body rotation

and translation) with arbitrary atom selection.
• New: Interactively compute RMSD between two
molecules (with arbitrary atom selection).
• Align all structures in a trajectory against the initial
Analysis and structure
Molecular • Interactively measure bond lengths, bond angles and
Manipulation torsion angles
• Dynamically adjust user selected torsion angles
• Display atom labels and coordinate axis
• Detect and display hydrogen bonds (using the energetic
criterion of Kabsch and Sander). NEW: Intermolecular
hydrogen bonds are determined in "real time".
• PDB files
• Compressed PDB files (using zlib) i.e. *.pdb.gz
• Directly query the Protein Data Bank and display the
Import Formats
resulting structure
• Paste temperature and occupancy PDB fields from the
windows clipboard
• Generate AVI movies from a molecular trajectory

• Print to any Windows supported printer and copy images to
Output Formats the Windows clip board
• Export images in BMP, PNG and Postscript (using vector,
not raster, output)
Procedure
Open Qmol.
• Go to File and open the PDB file of the protein using the option Open coord…
Options
• Go to options and click the following:
1) Secondary Structure
• Select the amino acid residues based on their conformation, to change the colour.
2) Animate
• Click Momentum first and then click Animate to rotate the protein molecule
automatically
Measure
• Go to Measure and click on the following:
1) Coordinates
• To view the coordinates of any 4 selected atoms.
2) Surface Area
• Surface area can be measured either by residues or by atoms.
Adjust
• Go to Adjust and click on the following:
1) Torsion Angle
• Click on any atom and select the option Torsion angle to make adjustments in the
torsion angle of the selected atom.
• 2)Atomic Radii
• Select Radius by element and choose the atom.
Render
Go to Render and we can render the following representations
• CPK
• Wireframe
• Points
• Sticks
• Ball and Stick
• Ribbon
• Trace
• Solid surface
• Mesh surface
• Dots surface
Click Display to view the Hydrogen bonds, Axes etc.
Color
• Go to Color and color the protein by
• Molecule
• Protein
• Surface
• Hydrogen bonds
Result
The Protein molecule was visualized and analyzed under Qmol with the following
results.
Fig 1: Sequence details for protein Myoglobulin
Fig 2: Structure details for protein Myoglobulin
Fig 3: Geometry for protein Myoglobulin
Visualization results
Fig 4: Color by secondary structure (coil (violet) helix (blue) turn (green))
Fig 5: Surface area by residue
Fig 6: Surface area by atom
Fig 7: Wire frame
Fig 8: The green color ring which fixes the torsion angle position
Fig 9: Active part of the protein is in CPK form
Fig 10: X, Y, Z coordinates
Fig 11: The Protein molecule (Myoglobin) with Ligand molecule
Fig 12: Information panel for myoglobin
Fig 13: Protein molecule myoglobulin without ligand and water molecule
Fig 14: The HEME which is present in the myoglobulin
RASMOL
Aim
To visualize the secondary structure of the protein molecule using RASMOL
visualization tool.
Description
Rasmol is a computer program written for molecular graphics visualization intended and
used primarily for the depiction and exploration of biological macromolecule structures,
such as those found in the Protein Data Bank. It was originally developed by Roger Sayle
in the early 90s. Historically, it was an important tool for molecular biologists since the
extremely optimized program allowed the software to run on modestly powerful personal
computers. Before Rasmol, visualization software ran on graphics workstations that, due
to their expense, were less accessible to scholars. Rasmol has become an important
educational tool as well as continuing to be an important tool for research in structural
biology.
Rasmol has a complex version history. Starting with the series of 2.7 versions, Rasmol is
licensed under a dual license (GPL or custom license RASLIC). Thus, Rasmol is along
with Molekel, Jmol and PyMOL among the few open source molecular visualization
programs available. RasMol includes a language for selecting certain protein chains, or
changing colors etc. Jmol has incorporated the RasMol scripting language into its
commands. Protein Databank (PDB) files can be downloaded for visualization from the
Research Collaboratory for Structural Bioinformatics (RCSB) bank. These have been
uploaded by researchers who have characterized the structure of molecules usually by X-
ray crystallography or NMR spectroscopy.
Procedure
Open Rasmol
• Go to file and open the PDB file of the protein using the option open.
Edit
• Go to edit and click the following options.
(1) Select all
(2) Cut
(3) Copy
(4) Paste
(5) Delete
Using these options, the protein are edited.
Display
• Go to display and click the following options.
(1) Wire frame
(2) Backbone
(3) Sticks
(4) Space fill
(5) Ball and Stick, etc.
Using this options, change the structure of the proteins can be changed.
Colors
• Go to display and click the following options.
(1) Monochrome
(2) CPK
(3) Shapely
(4) Group
(5) Chain
(6) Temperature
Using this options, the change in the color of the molecule are done based on
it shape and temperature.
Options
• Go to options and click the following options.
(1) Slabmode
(2) Hetero atoms
(3) Hydrogen
(4) Label
Using this, names of the atoms and number of hydrogen are known.
Command box
The RASMOL tool has some commands instead of option window.

Such a commands are,
(1) backbone on
backbone off
(2) colour
(3) background color on
background color blue
background color off
(4) connect on
connect off
(5) zoom on
zoom 150
zoom off
(6) dots on
dots off
(7) show information and sequence
(8) label on
label off
(9) ribbon on
ribbon off
(10) h bonds on
h bonds off
Angle window
Using this, window the calculation of the distance between the two atoms angle between
atoms and we can rotate the molecule also. It has following options such as,
(1) Distance
(2) Angle
(3) Dihedral
(4) Rotate all
(5) Rotate bond
(6) Rotate molecule
Output:
Fig 15: Protein-Agrin
Fig16: Background Colour Yellow

Command: Rasmol> Background Yellow
Fig17: Show Sequence result in command line

Command: Rasmol> show sequence
Fig 18: Rasmol>backbone on

Rasmol> backbone 50
Fig 19: Rasmol>hbonds on
Fig 20: Rasmol>hbonds 100
Fig 21: colour the whole molecule; Rasmol> Colour red
Fig 22: Rasmol> label on
Fig 23: Rasmol> ribbon 200
Fig 24: Rasmol> structure on
Fig 25: Rasmol> show symmetry
Fig 26: Rasmol> show information
Fig 27: Rasmol> restrict turns
Fig 28: Rasmol> restrict sheets
Fig 29: Rasmol> spacefill on
Fig 30: Rasmol > set axis
Fig 31: Rasmol :> zoom on Rasmol :> zoom 100
Fig 32: structure of ball and stick.
Result
The protein molecule was visualized using RASMOL tool and the results are saved.
• Number of chains: 2
• Number of groups: 131(75)
• Number of atoms: 1062(75)
• Number of bonds: 1083
• Number of h bonds: 91
• Number of helices: 4
• Number of strands: 13
• Number of turns: 10
PYMOL
Aim
To visualize the molecular structure of a protein molecule using PYMOL visualization
tool.
Description
PYMOL is an open-source tool to visualize molecules available from www.pymol.org. It
runs on Windows, Linux and MacOS equally well. PyMOL has excellent capabilities in
creating high-quality images from 3D structures, it has well-developed functions for
manipulating structures and some basic functions to analyze their chemical properties.
The possibilities to write scripts and plugins as well as to incorporate PyMOL in custom
software are vast and superior to most other programs. PyMOL has been written mostly
in the Python language www.python.org, while the time-critical parts of the system have
been coded in C. This way, Python programs interact most easily with the PyMOL GUI.
Procedure
• Since Pymol is a command and Menu oriented program, it follows two ways
including from loading the molecule.
• Pymol opens with two window of Menu or command window along with the
working or black window.
• The molecule can be loaded by either of the ways.
• Immediately after loading the molecule, the molecule will be added to the
working window by adding a frame to the earlier with the name of the protein.
• In the command box, it can get all the options to make a movie and also an added
option as builder to build amino acids or the organic groups to the native
molecule can also be added to the frame.
The menu bar comprises
File, Edit, Build, Movie, Display, Settings, Scene, Mouse, Wizard, Plugin, Help
Command Prompt
Loading the molecule load <path of the directory>
Coloring the molecule color <region>

Ray tracing ray
Displaying the atom display <region> <parameter>
Help help <command>
Some of the other commands used to redefine a molecule are:

View Movies imaging Maps
Selections Settings Atom Editing
Fitting Distances Stereo Symmetry
Scripts Language
Under the commands many sub-directions define the command preference in the header
command.
Builder
• The Builder features support the addition of chemicals of different kinds by
• Atoms, Fragments, Rings and also by the charge.
• The building can also done by creating bond, cycles and also edit by fixing the
hydrogen atoms.
• We can also build using protein classification with the addition of 20 amino acids.
Mouse mode
• Normally, Mouse mode in default is 3-button Editing holding the left, middle and
right along with wheel selection used with other keys as SHIFT, CTRL.
• Below the mouse mode, movie play option with initial, previous, stop, play, next,
last and sequence set up in the window with symbol ’S’.
• Animation can be done with momentum selection at the last of the option ▼.
Keyboard commands and Modifiers

ESC Toggle onscreen text
INSERT Toggle rocking
LEFT ARROW Go backward one frame, when editing, go backward one character
RIGHT ARROW Go forward one frame, when editing, go forward one character
HOME, END Go to the beginning or end of a movie
Command Entry Field in the Internal GUI (black window)

TAB Complete command or filename (like in tcsh or bash)
CTRL-A Go to the beginning of the line
CTRL-E Go to the end of the line
CTRL-K Delete through to the end of the line
Command Entry Field on the External GUI (gray window)

CTRL-C These operating system –provided cut and paste functions
CTRL-V will only work in the external GUI command line
Short cut selections for Visualization

All the molecule or the loaded information is given with specific default options to
work with it as:

Actions
Zoom Centre Origin Preset Find Hydrogens Masking
Movement Compute
Show as
Lines Sticks Ribbon Cartoon Label Cell Dots Spheres Mesh
Surface
Hide
All the functions in show as.
Label
Residues Chains Segments Atom Name Element Symbol b-Factor
Occupancy
Color by
Element Chain SS
Output
Fig 33: Viral core structure of HIV
Fig 34: Ribbon structure
Fig 35: B factor putty
Fig 36: B factor
Fig 37: Chain structure
Fig 38: Mesh structure
Fig 39: Surface structure
Fig 40: After removing water molecule
Fig 41: ball and stick model
Fig 42: Find – polar contacts
Fig 43: Numbering the atoms
Fig 44: Ligand at solid states
Fig 45: Cell
Fig 46: Symmetry relation of proteins
Fig 47: Vaccum electrostatics
Result
The core protein of the HIV is visualized using the pymol –visualization tool, and the
Ligand molecule of the protein,secondary structure of the protein,b factor ,and number
the atoms are done using the pymol and the results are saved.
SWISS PDB VIEWER
Aim
To visualize the protein molecule using Swiss PDB Viewer and study its structure
Tool Description
Swiss-PDB viewer also called as Deep view. Deep view was developed by Nicolas
Guix.Swiss PDB viewer is tightly linked to Swiss model, an automated homology
modeling server developed within the SIB (Swiss Institute of Bioinformatics) at the
structural bioinformatics group at the Biozentrum in Basel. Deep view is an application
that provides a user friendly interface allowing analyzing several protein at the same
time. The protein can be superimposed in order to deduce structural alignments and
compare their active site or any other relevant parts. Amino acids mutation, hydrogen
bonds, angles and distance between atoms are available. Swiss PDB viewer can also read
electron electron density maps. Swiss pdb viewer allows options to find bond length,
bond angle, torsions, mutate etc of the particular protein.
Procedure
1. Go to Swiss PDB Viewer
2. To download the sequence into Swiss PDB Viewer goes to file-open-pdb file.
3. The molecule is shown as 3D structure
4. The options file, edit, select, build, tools, fit, display, colors, preference, swiss
model and windows are available to improve the view of the structure and for
better understanding.
Tool bar options
5. The tool bar is available as default in the deep view window
6. The tool bar is divided into three regions based on their work.
Centering tool
7. The centering tool is used to center the molecule on the graphics window.
Molecule manipulation
8. To move the molecule in the graphics window.
9. To zoom in and zoom out the molecule
10. To rotate the molecule in the graphics window
Measuring tools
11. To find the distance between two atoms.
12. Select the icon on the tool bar and then select the two atoms one after the
other by clicking on the molecule
13. The distance between the two atoms selected is displayed on the screen.
14. To find the angle between three atoms
15. Select the icon on the tool bar and then select the three atoms one after the
other by clicking on the molecule
16. The distance between the three atoms selected is displayed on the screen
17. To measure the dihedral angles
18. Select the icon on the tool bar and then select an atoms by clicking on the
molecule
19. The omega, phi, psi angles of the atom picked is given just below the toolbar.
20.We can also pick four atoms from the molecule there by measuring the torsion
angle .
21. To find the provenance of an atom
22. Select the icon from the toolbar and select the atom by clicking on the
molecule.
23. The name, group, chain and the atom of the molecule is displayed on the screen
for the selected atom
24. To display or undisplay the atoms
25. Select the icon from the toolbar and select the atom by clicking on the
molecule.
26. Display/undisplay or select groups that are/aren’t at a certain distance from an
atom selected.
27. To center the molecule on one atom
28. Select the icon from the toolbar and and select the atom from the molecule
to center the molecule based on the molecule selected.
29. To fit one molecule over the other
30. Two molecules are loaded and then select the icon and select the atoms for the fit.
31. To mutate the molecule
32. Select the icon from the tool bar and select the atom to be mutated in the
molecule
33. The particular atom is mutated from the molecule
34. To torse the angles in the molecule
35. Select the icon for torsion from the toolbar

36. Select the atom at which the torsion is to made from the graphics window.
37. Arrows appear near the icon which for gross and small torsions.
38. The torsion angle can be adjusted with the arrows.
Output:
Fig 48: Taken protein: heparin
Fig 49: Additional molecule added: Agrin protein
Fig 50: Separated view Agrin in green Colour
Fig 51: Agrin red colour, heparin green Colour
Fig 52: Molecule with backbone structure-Agrin
Fig 53: Two Molecules in visual view of Ribbon type
Result
The protein structure viewed was AGRIN protein and HEPARIN protein. By the Swiss
pdb viewer the distance between the proteins, polar amino acids and non polar amino
acids are known and the protein molecule was visualized using Swiss tool and the results
are saved.

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SeLnIkRaJ www.selnikraj.110mb.

com Visit this and Get more

Bioinformatics Visualization Tools

It supports the following

• Wire frame, Stick figure, Ball and stick, Point, Space-

• New: Superimpose two molecules (by rigid body rotation

• Generate AVI movies from a molecular trajectory

Fig 1: Sequence details for protein Myoglobulin

Fig 2: Structure details for protein Myoglobulin

Fig 3: Geometry for protein Myoglobulin

Fig 5: Surface area by residue

Fig 6: Surface area by atom

Fig 7: Wire frame

Fig 9: Active part of the protein is in CPK form

Fig 10: X, Y, Z coordinates

Fig 11: The Protein molecule (Myoglobin) with Ligand molecule

Fig 12: Information panel for myoglobin

Fig 14: The HEME which is present in the myoglobulin

The RASMOL tool has some commands instead of option window.

Fig 15: Protein-Agrin

Fig16: Background Colour Yellow

Fig17: Show Sequence result in command line

Fig 18: Rasmol>backbone on

Fig 19: Rasmol>hbonds on

Fig 20: Rasmol>hbonds 100

Fig 21: colour the whole molecule; Rasmol> Colour red

Fig 22: Rasmol> label on

Fig 23: Rasmol> ribbon 200

Fig 24: Rasmol> structure on

Fig 25: Rasmol> show symmetry

Fig 26: Rasmol> show information

Fig 27: Rasmol> restrict turns

Fig 28: Rasmol> restrict sheets

Fig 29: Rasmol> spacefill on

Fig 30: Rasmol > set axis

Fig 31: Rasmol :> zoom on Rasmol :> zoom 100

Fig 32: structure of ball and stick.

Coloring the molecule color <region>

Some of the other commands used to redefine a molecule are:

Keyboard commands and Modifiers

Command Entry Field in the Internal GUI (black window)

Command Entry Field on the External GUI (gray window)

Short cut selections for Visualization

work with it as:

Fig 33: Viral core structure of HIV

Fig 34: Ribbon structure

Fig 35: B factor putty

Fig 36: B factor

Fig 37: Chain structure

Fig 38: Mesh structure

Fig 39: Surface structure

Fig 40: After removing water molecule

Fig 41: ball and stick model

Fig 42: Find – polar contacts

Fig 43: Numbering the atoms

Fig 44: Ligand at solid states

Fig 45: Cell

Fig 46: Symmetry relation of proteins

Fig 47: Vaccum electrostatics

SWISS PDB VIEWER

35. Select the icon for torsion from the toolbar

Fig 48: Taken protein: heparin

Fig 49: Additional molecule added: Agrin protein

Fig 50: Separated view Agrin in green Colour