BIRLA INSTITUTE OF SCIENTIFIC RESEARCH, JAIPUR
Summer Training MAY-JULY, 2018
Summer Training MAY-JULY, 2018
Section - 1 : Protein Structure Visualization and Analysis
Lab1: Visualization of Protein using RasMol
Rasmol is a computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecule structures.
- 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:
- M(enu) File-- Open.
- Select 1d66.pdb(gal4 transcriptional regulator complexed to DNA).
- 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
(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).
(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 ';'
- rotate x
/ rotate y / rotate z
- rotate x 50; rotate y 90; zoom 250;
- select all / select * : to select all atoms
- select none : to deselect selected atoms
- select hetero : to select molecules except amino acids (DNA/RNA etc.)
:three letter code of amino acid to select all this amino acids
/ labeltoggle label/ name of selected atom in molecule :
:to label selected atom(s) with some name.
- select command will work with following parameters -
- set axis
/ set axisshow 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
- 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
- zap : deletes molecule(s) from viewer
:to change background color
:to change color of selected atom
/ dotsto show/ hide vander wall surface on atoms :
/ hbondsto show/ hide hydrozen bonds present in molecule. :
/ ssbondsto show/ hide di-sulphide bonds present in molecule :
Section - 2 :Protein structure analysis and secondary structure prediction
- Take a protein sequence in FASTA format whose structure is to be modelled. This is our 'Target Sequence'.
- Now go to the webpage http://swissmodel.expasy.org/
- Paste target sequence into swiss model workspace in FASTA format
(you can also upload target sequence )
you can provide a Project title and email-id-
You have 2 options now you can either search for templates or build models directly
- you can see result after a while
- We can also download the detailed results
Section - 3: Protein Structure Validation
The Structure Analysis and Verification using SAVES Server
- Open SAVES SERVER webpage: http://services.mbi.ucla.edu/SAVES/
- Upload the PDB file.
- RUN all programs
Press the button 'build model'.
Swissmodel provide 3 best results according to their score
It provide- Sequence identity, Alignment and Structure