Lab6Displaying Biomolecule Using Rasmol

Protein Structure and Function

Oct 18th, 2007

http://202.120.45.17/course/intro/lab6.htm

The structure allows better understanding of the structure-function relationship, and is an important starting point for many kinds of research.

Tools - PC tools: rasmol, pymol, SwissPDBviewer

(very powerful and contains many functions, i.e., homology modeling)

- Web-based tools: Protein Explore

Protein visualization

Protein Data Bank http://www.rcsb.org

Search Field

calmodulin

Rasmolhttp://www.openrasmol.org

Protein Data Bankhttp://www.rcsb.org

Protein PDB ID

CD2 1hngLysozyme 1lz1GFP 1b9cROP 1f4n-Lactalbum 1hmlCalmodulin (apo) 1cfcCalmodulin (Ca2+) 3cln

RasMol: main menu

RasMol: Display

RasMol: Display

RasMol: Display

RasMol: Display

RasMol: Display

RasMol: Display

RasMol: Display

RasMol: Color

RasMol: Option

RasMol: Option

RasMol: Option

RasMol: Option

RasMol: Option

RasMol: Command line

The Select Command

Primitive expressions Predefined sets Comparison operators Within expressions logical combination of all above

mentioned.

The select command Atom number - select AtomNo.=102 Residue – select Val52 (select resno=52) Chain id – select :a List of residue numbers – select 14,92, 46 Range of atom numbers – select atomno=>35 A wildcard can be used to specify a whole field: -- * Any number of characters

Atom or residue type – select *.sg (this will select all Sulphur atoms in Cistein’s side

chain) -- ? Single character wildcard – select ser70.c? –

will select all carbons in all serine residues.

The within expressions defines the neighbors of a given set of atoms:

select within (4.0, backbone)

Distance: the cut-off in Å

Where containing

decimal point

Set of atoms

Example : all atoms not further than 3.5Å from Ala35:

Select within (3.5, Ala35)

The predefined sets are groups of atoms given the definite names:

select helix

select hoh (water molecules)

select protein

There is a list with the predefined sets

In order to display only what we selected, use the command:

restrict selected

Boolean Expressions

select tyr and :a → all tyr in ‘a’ chain

select tyr or :a → all tyr in the molecule and all ‘A’ chain

select not (try,:a) → all the molecule beside try and ‘a’ chain

Movement in RasmolRotation

Change Viewing Size

Horizontal MovementVertical Movement

Left Click

Shift Key + Left Click

Rotation

Change Viewing Size

Horizontal MovementVertical Movement

Movement in Rasmol

Right Click

To select a residue (# 78) select 78To select an atom (atom# 122) select atomno=122To change color of display color blueTo change the background color background whiteTo select one of the option from list select acidic

Exercise• Load the 1GCD.pdb (file → open)

• Go over the display menu and try all of the options

• Set the display on wireframe and try the color menu

• Set the display on cartons and try the color menu again

• Than, try the command line:

ribbons

wireframe 40

spacefill 120

spacefill off

select Ser

spacefill 150

color cpk

zoom 200

select all

wireframe 40 (If it doesn't work, do Display => wireframe in the menu)

color chain

hbonds on (how much Hbonds are their?)

hbonds 30

color hbonds green

hbonds off

select hetero and not hoh

spacefill 120

color CPK (Touch the selected atoms with the mouse and look on the command line)

select water

spacefill 120

color magenta

select ligand

spacefill 300

Question Which atoms are present besides the protein? Show only them.

Show only the ligand (inhibitor) and the oxyanion pocket (gly193, ser195)

Color them in CPK. Display the inhibitor in sticks and the protein’s oxyanion pocket in balls and sticks.

Label the residues and the inhibitor (not every atom, just the number and type)

Measure the distance between the gly’s nitrogen and the ligand’s oxygen

Select all the protein. How many secondary structures does the protein contains?

Show only the helixes, center them on the screen.

select the resides that are within the radius of 8.0 Å from the inhibitor. Display only them and the inhibitor. Color the hydrophobic residues in blue and charged residues in magenta. What do you see?

select asp102,his57,ser195 or ligand

restrict selected

center selected

color CPK

Display => balls and sticks (on the menu)

labels on

labels off (try also the option menu- labels, what is the difference?)

Select ligand

Display sticks

set picking distance (pick a pair of atoms which you want to know their distance)

set picking distance off