Lab6

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Lab6 Displaying Biomolecule Using Rasmol
Protein Structure and Function Oct 18th, 2007
http//202.120.45.17/course/intro/lab6.htm
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Protein visualization

• 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

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Protein Data Bank http//www.rcsb.org
Search Field calmodulin
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Rasmol http//www.openrasmol.org Protein Data
Bank http//www.rcsb.org Protein PDB
ID CD2 1hng Lysozyme 1lz1 GFP 1b9c ROP
1f4n ?-Lactalbum 1hml Calmodulin
(apo) 1cfc Calmodulin (Ca2) 3cln
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RasMol main menu
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RasMol Display
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RasMol Display
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RasMol Display
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RasMol Display
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RasMol Display
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RasMol Display
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RasMol Display
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RasMol Color
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RasMol Option
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RasMol Option
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RasMol Option
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RasMol Option
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RasMol Option
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RasMol Command line
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The Select Command

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

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The select command

• Atom number - select AtomNo.102
• Residue select Val52 (select resno52)
• Chain id select a
• List of residue numbers select 14,92, 46
• Range of atom numbers select atomnogt35
• 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 Cisteins side
  chain)
• -- ? Single character wildcard select
  ser70.c? will select all carbons in all
  serine residues.

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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)
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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
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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

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Movement in Rasmol
Rotation
Horizontal Movement Vertical Movement
Change Viewing Size
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Movement in Rasmol
Left Click
Rotation
Right Click
Shift Key Left Click
Horizontal Movement Vertical Movement
Change Viewing Size
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To select a residue ( 78) select 78 To select
an atom (atom 122) select atomno122 To change
color of display color blue To change the
background color background white To select one
of the option from list select acidic
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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

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select all wireframe 40 (If it doesn't work, do
Display gt 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
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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 proteins 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 glys nitrogen
  and the ligands 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?

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select asp102,his57,ser195 or ligand restrict
selected center selected color CPK Display gt
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