molecular viewers

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Molecular viewers Preston University Islam abad

Protein visualizationsAmino acid SequencesTranslated SequencesSignature Sequences----Motifs

and PatternsConserved Sequences among

Orthologues and Paralogues

PROSITE---a pattern identifier

A short guide to Molecular Visualization using some of the tools in the Jmol program

http://jmol.sourceforge.net/

The Jmol applet opens automatically from the Protein Data Bank

www.pdb.org brings you to the U.S. portal for the world-wide PDB

The Protein Data Bank is an international consortium

Structures submitted to the Protein Data Bank have a 4-character accession number

3COQ

Let’s look for Gal4p, which has the PDB accession number 3COQ(You can find PDB numbers on the Protein tab at SGD)

Begin your project by obtaining the PDB file for your protein

Summary page for PDB records includes the literature reference and MANY links

Click here to begin using Jmol

Drag the structure with your mouse

Default Jmol view

Uses the Cartoon scheme

With Structure colors

Structure colorsα-helices are pinkCoils are whiteβ-sheets are gold (none shown)DNA is purple

Click on Jmol_S to access commands that will customize your structure

Begin by using the Select command

Jmol can work on the whole structure of parts of the structure at one time

In the next few slides we’ll work on only the protein structure

Select “Protein”Next, select “All”

Allows you to work on the whole structure, or just the protein (or nucleic acid or cofactors)

First, we’ll choose a scheme to display the protein.

Begin by choosing STYLE at the main menu.

Let’s look at the structure with these different rendering schemes

Spacefill Ball and stick Sticks

Wireframe Cartoon Trace

Cartoon and trace are shown in structure colors

Gal4p is shown in several schemes in either CPK or structure colors

CPK (Corey-Pauling-Koltun ) is a color scheme for atoms (C=grey; O=red; N=blue; S=yellow)

Add some color – choose color from the main menu

Atoms can be colored with a color of your choice or with a coloring scheme

Group color schemeN-terminal is blue (cold)

C-terminal is red

Amino acid scheme

Gives a different color to each amino acid

Chain color schemeEach polypeptide gets a

different color (Gal4p is a dimer)

Finishing the image

Select the nucleic acid – choose the ball and stick rendering scheme (default colors are CPK)

Small molecules in the structures are considered “Hetero” atoms

After selecting hetero, we’ll use the spacefilling scheme for the Zn atoms in the Zn-fingers and color them orange

In addition to Zn atoms, a molecule of 2-methyl-2,4-pentanediol is bound to the structure

Once you’re finished your structure, it can be exported in a variety of file formats

Thanks