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BIRLA INSTITUTE OF SCIENTIFIC RESEARCH, JAIPUR

Summer Training Exercises

Day4

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Section - 1 : Protein Structure Visualization and Analysis

Lab1: Visualization of Protein using RasMol

Introduction

Rasmol is a computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecule structures.

Getting Started

  • Start Rasmol from your computer's Dektop.

  • This will open two Windows (one Black window, another white command-line window)

  • Commands below preceded by M are best done from the pull-down Menus. Command NOT preceded by M must be typed in the white command-line window. (RasMol has two windows, one black and one white. On windows, the white command-line window starts minimized. look for it on the taskbar.

  • Run RasMol, and do:

  1. M(enu) File-- Open.

  2. Select 1d66.pdb(gal4 transcriptional regulator complexed to DNA).

  3. Trasform viewer space

    • Shift + left mouse button : zoom in/ zoom out space

    • Shift + right mouse button : rotate space in view axis

    • left mouse button : rotate space in all axis

    • right mouse button : pan/shift space in view axis

  4. Change the display of protein

    (A). M(enu) Display -->

    • Wireframe : protein in wireframe mode

    • Backbone : only backbone (peptide bond chain) will be displayed

    • Sticks : protein in sticks form mode

    • Spacefill : residues in ball form

    • Ball & Stick :atoms in ball form and bonds in stick form

    • Ribbons : protein in chain form (best mode to visualize secondary structures)

    • Strands : ribbon in wireframed strand form

    • Cartoons : thick ribbons with some shapes displaying SS.

    • Moleculer Surface : protien in solid surface form. heavy in render.


    (B). M(enu) Colours -->
    • (various option to visualize protein in different colors).


  5. Some Commands:

    (Do not write '< >' symbols in command line of RasMol used below here. These are only for an indication that here a value must be written. Press 'ENTER' key after each command given)-

    Note: You can give more than one command at a time by seperating them by semicolon ';'
    • reset

    • rotate x / rotate y / rotate z

    • zoom

    • rotate x 50; rotate y 90; zoom 250;


  6. Select Commands:
    • select all / select * : to select all atoms

    • select none : to deselect selected atoms

    • select hetero : to select molecules except amino acids (DNA/RNA etc.)

    • select : three letter code of amino acid to select all this amino acids

    • label / label : toggle label/ name of selected atom in molecule

    • label : to label selected atom(s) with some name.

    • select command will work with following parameters -

    AT Acidic Acyclic Aliphatic Alpha Amino
    Aromatic Backbone Basic Bonded Buried CG
    Charged Cyclic Cystine Helix Hetero Hydrogen
    Hydrophobic Ions Large Ligand Medium Neutral
    Nucleic Polar Protein Purine Pyrimidine Selected
    Sheet Sidechain Small Solvent Surface Turn
    Water

  7. Set Commands:
    • set axis / set axis : show hide xyz axis in viewer

    • set ambient : set constrast to shaded object (value: 0-100)

    • set background : changes background color

    • set boundbox / : sets boundary box to molecules

    • set fontsize : set fontsize of labels

    • set picking distance : pick any two atoms and get distance between them

    • set picking angle : pick any three atoms and get angle among them

    • set picking torsion : pick any four atoms and get torsion angle among them

    • Below parameters are used with 'set' command

    Ambient Axes Background BackFade BondMode Bonds BoundBox Cartoon
    CisAngle Display FontSize FontStroke HBonds Hetero HourGlass Hydrogen
    Kinemage Menus Monitor Mouse Picking Play... Radius Record...
    ShadePower Shadow SlabMode Solvent Specular SpecPower Stereo SSBonds
    Strands Transparent UnitCell VectPS Write

  8. Show commands:
    • show information : shows information of molecule

    • show phipsi : shows phi psi angle of a peptide bond

    • show rotation : shows rotation angle (x,y,z) of space

    • show translation : shows x , y position of space

    • show sequence : shows sequence of protein


  9. Other Commands:
    • zap : deletes molecule(s) from viewer

    • background : to change background color

    • color :to change color of selected atom

    • dots / dots : to show/ hide vander wall surface on atoms

    • hbonds / hbonds : to show/ hide hydrozen bonds present in molecule.

    • ssbonds / ssbonds : to show/ hide di-sulphide bonds present in molecule




    10. Section - 2 :Protein structure analysis and secondary structure prediction

    Lab1: Protein structure analysis using PIASP2

    PIASP2

    A Tool developed by BISR for protein parsing and analysing/ predicting its secondary structure.


    http://bioinfo.bisr.res.in/cgi-bin/project/piasp2/index.cgi

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