Transcript Document

Lab6
Displaying Biomolecule Using Rasmol
Protein Structure and Function
Oct 18th, 2007
http://202.120.45.17/course/intro/lab6.htm
Protein visualization
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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 Data Bank
Search Field
calmodulin
http://www.rcsb.org
Rasmol
http://www.openrasmol.org
Protein Data Bank
http://www.rcsb.org
Protein
PDB ID
CD2
Lysozyme
GFP
ROP
-Lactalbum
Calmodulin (apo)
Calmodulin (Ca2+)
1hng
1lz1
1b9c
1f4n
1hml
1cfc
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
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Primitive expressions
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Predefined sets
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Comparison operators
Within expressions
logical combination of all above mentioned.
The select command
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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
Set of atoms
Where containing
decimal point
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
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select tyr and :a → all tyr in ‘a’ chain
select tyr or :a → all tyr in the molecule
and all ‘A’ chain
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select not (try,:a) → all the molecule
beside try and ‘a’ chain
Movement in Rasmol
Rotation
Horizontal Movement
Vertical Movement
Change Viewing Size
Movement in Rasmol
Rotation
Left Click
Right Click
Shift Key + Left Click
Horizontal Movement
Vertical Movement
Change Viewing Size
To select a residue (# 78)
To select an atom (atom# 122)
To change color of display
To change the background color
To select one of the option from list
select 78
select atomno=122
color blue
background white
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
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Which atoms are present besides the protein? Show only them.
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Show only the ligand (inhibitor) and the oxyanion pocket (gly193, ser195)
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Color them in CPK. Display the inhibitor in sticks and the protein’s oxyanion
pocket in balls and sticks.
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Label the residues and the inhibitor (not every atom, just the number and
type)
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Measure the distance between the gly’s nitrogen and the ligand’s oxygen
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Select all the protein. How many secondary structures does the protein
contains?
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Show only the helixes, center them on the screen.
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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