Included here are image files and descriptions on how to create them. Some
of the tools mentioned are found only on an SGI machine, but there may be
equivalent tools on other machines. These tools include:
blend
assemble
izoom
paste
snapshot
Most Unix machines with manual pages may give you information you need if
you ask for a
man -k image",
and see what image tools are available.The images here are in TIFF format
and are the files that end in ".tiff". For each ".tiff" file, there is a
corresponding ".readme" file that describes the scientific model system
and the procedure for creating the image file. TIFF files can be viewed
on SGIs with
imgview
on DEC Alphas with
xv
(provided with the MidasPlus DEC distribution in /usr/local/midas/bin);
and on NeXTs simply by double clicking on the ".tiff" file.
On DEC Alphas, the images frequently look better if the gamma correction
factor for the 'xv' viewing program is changed to 1.7. This can be accomplished by using the
right mouse button (in 'xv') to bring up the "controls" panel. Pick the
"ColEdit"button to bring up the Color Editor panel. In the "Intensity" field,
click the "Gam" button and type in a value of 1.7.
bilayer
Model system:
Model of colicin Ia in its membrane-associated state, prior to insertion
into the bilayer.
Emphasized image creation method:
Using articial PDB files for special effects.
cartoon
Model system:
The structure of Bacteriorhodopsin.
Emphasized image creation method:
Using (now obsolescent) Ribbon program, and Ilabel
conic_and_neon
Model system
Homeodomain protein segment bound to DNA
Emphasized image creation method
Mixing Neon "stick" representation with Conic "sphere" representation
crosseye_density
Model system:
Custom designed peptide that forms a 4 helix bundle
Emphasized image creation method:
Creating stereo views
custom_colors
Model system:
Slip-Loop DNA model
Emphasized image creation method:
Specifying custom colors for use in images
density_and_helices
Model system:
Bacteriorhodopsin and microscopic and xray density
Emphasized image creation method:
Using Density delegate to show electron density contours
depth_cue:
Model system:
Rat Trypsin versus Bovine Trypsin
Emphasized image creation method:
Using depthcuing in Neon
label3d
Model system:
Thymidylate Synthase-DHFR complex
Emphasized image creation method:
Making stereo image with stereo labels
paint
Model system
Alpha Lytic Protease and two potential substrates
Emphasized image creation method:
Using paint programs (if available) for special effects
ribbonjr
Model system:
Slip-Loop DNA model
Emphasized image creation method:
Using various Ribbonjr options
sliced_conic
Model system:
Acetylcholine Receptor
Emphasized image creation method:
Cutting through Conic images to show interiors
transparency1
Model system:
DIP-inhibited Trypsin, space filling and stick models
Emphasized image creation method:
Creating "semi-transparent" images
transparency2
Model system:
HIV-1 Protease substrate comparison
Emphasized image creation method:
Additional "semi-transparent" image techniques
two_views_ipaste
Model system:
E.coli Bacteriorhodopsin and density
Emphasized image creation method:
Collating multiple images
walleye_density
Model system:
As for "crosseye_density" image
Emphasized image creation method:
Creating stereo view