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
Rasmolhttp://www.openrasmol.org
Protein Data Bankhttp://www.rcsb.org
Protein PDB ID
CD2 1hngLysozyme 1lz1GFP 1b9cROP 1f4n-Lactalbum 1hmlCalmodulin (apo) 1cfcCalmodulin (Ca2+) 3cln
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
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