Molecular Visualization

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Molecular Visualization
Molecular Visualization
Computational Chemistry 5510 Spring 2006 Hai Lin
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How to Represent a Molecule?
Sticks
Lines
Ball Sticks
Small Molecules Example C6H6
Dots
Sapcefill
BSD
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How to Represent a Molecule? (2)
Biological molecules can be represented in the
same way, but other represntations are also
helpful.

• Proteins
• Carbohydrates
• Nucleic Acids
• Lipids

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Protein Structure

• Building Blocks
• 20 amino acids found in proteins
• Primary Structure
• Sequence of the amino acids in a peptide chain
• Secondary structure
• Includes a helix, b sheets, hairpin turns, etc.
• Tertiary structure
• Overall folding of peptide chain in 3D space
• Quaternary structure
• Combination of several subunits packing together

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PDB File Format
Example alanin.pdb in the VMD Distribution
REMARK FILENAME"/usr/people/nonella/xplor/benchma
rk1/ALANIN.PDB" REMARK PARAM11.PRO ( from PARAM6A
) ... REMARK JACS
1033976-3985 WITH 1-4 RC1.80/0.1 REMARK
DATE16-Feb-89 112132 created by user
nonella ATOM 1 CA ACE 1 -2.184
0.591 0.910 1.00 7.00 MAIN ATOM 2
C ACE 1 -0.665 0.627 0.966 1.00
0.00 MAIN ATOM 3 O ACE 1
-0.069 1.213 1.868 1.00 0.00
MAIN ... ATOM 64 N CBX 12 8.610
8.962 9.714 1.00 0.00 MAIN ATOM 65
H CBX 12 8.050 8.324 9.225 1.00
0.00 MAIN ATOM 66 CA CBX 12
9.223 8.571 11.014 1.00 0.00 MAIN END
Comments
Coordinate Information
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PDB File Format (2)
(http//www.umass.edu/microbio/rasmol/pdb.htm)
RTyp Num Atm Res Ch ResN X Y Z
Occ Temp PDB Line ATOM 1 N ASP L 1
4.060 7.307 5.186 1.00 51.58 1FDL
93 ATOM 2 CA ASP L 1 4.042 7.776
6.553 1.00 48.05 1FDL 94 RTyp Record
Type Num Serial number of the atom. Each atom
has a unique serial number. Atm Atom name (IUPAC
format). Res Residue name (IUPAC format). Ch
Chain to which the atom belongs (in this case, L
for light chain of an antibody). ResN Residue
sequence number. X, Y, Z Cartesian coordinates
specifying atomic position in space. Occ
Occupancy factor Temp Temperature factor (atoms
disordered in the crystal have high temperature
factors). PDB The PDB data file unique
identifier. Line Line (record) number in the
data file.
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An Example Alanine Peptide
Lines
Sticks (Bonds)
Ribbons
Cartoon
Surface
Balls Sticks Ribbons
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More Examples Proteins
Cytochrome P450cam
Avidin-Biotin Complex http//www.ks.uiuc.edu/Resea
rch/vmd/gallery/
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More Examples DNA
A DNA Piece Ribbons
DNA-Protein Complex Solvated in
Water http//www.ks.uiuc.edu/Research/vmd/gallery/

Lines
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Practise with VMD

• VMD is a widely used program for biomolecule
  visualization.
• http//www.ks.uiuc.edu/Research/vmd/
• VMD has been installed in the PCs. Double click
  the icon to start.
• The VMD directory is C\Program Files\University
  of Illinois\VMD.
• The protein examples are under the proteins
  subdirectory.
• An online tutorial can be found at
• http//www.ks.uiuc.edu/Training/Tutorials/vmd/tuto
  rial-html/index.html
• Do you enjoy the stereo view? It is Fun!

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Your Homework

• Practise VMD
• Read/Load Molecules
• Different Kinds of Representations
• Uses of the Mouse
• Make a Picture for HIV-1 Protease Complexed with
  a Tripeptide Inhibitor (PDB code 1A30
  http//www.rcsb.org/pdb/explore.do?structureId1A3
  0) or any other molecule that you are interested
  in.