Graphical representation of structural data
or
One picture is worth a thousand words
Problem I: How to analyze complex 3D models
Some approaches:
View simplified models
backbone as ribbon
(
sample MIDAS input file
)
helices as cylinders
molecular surface only
Use different
colors
to view
residue type (charged, hydrophobic etc.)
B-factor
(by-atom or by-residue)
real-space correlation coefficient
sequence number
accessibility
surface curvature
different molecules
Automatic display of hydrogen bonds
Identify & display internal cavities (solvent or ion sites)
Problem II: How to convey complex 3D information in 2D (on paper)
Some approaches:
Simplified models (
backbone ribbon
,
molecular surface only,
thin slab for density
)
Stereo view
(adds back 3
rd
dimension to a limited extent)
Depth-cueing
Shadowing
Plot property vs. residue number
B-factor
RMS deviation
between two models
Side-by-side
of the same region
Show crystallographic
symmetry
Simplified schematic
with distances etc.
Overview of graphics applications
Structural models
ribbon
wire-frame
ball & stick
space-filling (or CPK)
tangible (HIV protease dimer)
Surfaces
van der Waals surface
solvent-accessible surface
contact surface between two molecules
color surfaces according to properties
electrostatic potential
B factor
polarity
accessibilty
surface curvature
relative homology/identity
Electron densities
2F
o
- F
c
F
o
- F
c
Overview of programs
Interactive Programs
IRIX
DEC-UNIX
PC
LINUX
MAC
Website
Rasmol
X
X
X
X
X
http://science.glaxowellcome.com/science/rasmol/
Molscript
X
X
http://www.avatar.se/molscript/
MSMS
X
X
X
http://www.scripps.edu/pub/olson-web/people/sanner/html/msms_home.html
Setor
X
offline -> new OpenGL version "soon"
Grasp
X
http://trantor.bioc.columbia.edu/grasp/
VMD
X
X
X
http://www.ks.uiuc.edu/Research/vmd/
Swiss PDB Viewer
X
X
X
X
http://www.expasy.ch/spdbv/mainpage.html
Midas-Plus
X
X
http://www.cgl.ucsf.edu/Outreach/midasplus.html
Chimera
X
X
X
http://www.cgl.ucsf.edu/chimera/
Mac/PC Molecule
X
http://www.blc.arizona.edu/linus/linus.html
Molview
X
X
http://bilbo.bio.purdue.edu/~tom/
Molmol
X
X
X
X
http://www.mol.biol.ethz.ch/wuthrich/software/molmol/
Spock
X
X
X
http://quorum.tamu.edu/spock/
Insight-II
X
http://www.cmc.uab.edu/ribbons/ribbons.html
Ribbons
X
X
X
X
http://www.cmc.uab.edu/ribbons/
BobScript
X
http://orval.rega.kuleuven.ac.be/~robert/BobScript/
MAIN
X
X
http://www-bmb.ijs.si/
CHAIN
X
http://seqaxp.bio.caltech.edu/www/hhmi_manuals/chain.txt
O
X
X
X
X
http://alpha2.bmc.uu.se/~gerard/manuals/gerard_manuals.html
Renderers
Raster3D
X
X
X
X
http://www.bmsc.washington.edu/raster3d/raster3d.html
POV-Ray
X
X
X
X
X
http://www.povray.org/
RayShade
X
X
X
X
X
http://www-graphics.stanford.edu/~cek/rayshade/rayshade.html
References & weblinks
O for dummies
etc. by G.J. Kleywegt
Ribbons
by M. Carson,
Meth. Enz.
277
, 493-505 (1997).
Journal of Molecular Graphics and Modelling
.
Next: Crystallographic data reporting
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