UCSF MidasPlus Sample Images
Included here are image files and descriptions on how to create them.
Some of the tools mentioned are found only on SGI workstations,
but there may be equivalent tools on other machines.
These tools include:
- blend -- linearly interporlate two images
- assemble -- assemble an array of smaller images
- izoom -- magnify or shrink an image
- imgview -- display image files
- imgsnap -- save all or part of the screen in an image file
Each image page shows a low-resolution version of the image
and describes the scientific model system and
the procedure for creating the image file.
You can pick the JPEG or TIFF versions to see the 24-bit versions
of the images (JPEG images are smaller than the TIFF versions).
Notes on viewing these images
Unfortunately,
the sample images provided here will look different
on different brands of workstations.
This is because of the different methods that vendors
use for correcting the non-linearity of the CRT display,
also known as ``gamma correction.''
Some vendors, such as Silicon Graphics,
provide gamma look up tables that are loaded with values
to do the proper gamma correction.
Other vendors don't do anything about gamma correction.
The result is that images such as these that were created
on a Silicon Graphics workstation will look too dark
when viewed on SUNs, MACs and PCs,
and images that you might find elsewhere that were created on
these other systems will look too light when viewed
on an SGI workstation.
As Paul Haeberli from SGI says
``AAAAARRGH! This is such an INCONVENIENCE!''
Unfortunately, there are no good solutions to this problem.
If you are using a computer that doesn't do any gamma correction,
you can try adjusting the brightness and contrast on your monitor.
On workstations like Digital Equipment Alphas,
when viewing the images with the ``xv'' viewing program,
we suggest that you change the gamma correction factor to 2.0.
(This can be done from "controls" menu 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 2.0.)
If you want to read more about display gamma correction,
take a look at Paul Haeberli's
Grafica Obscura.
Paul includes a brightness test pattern that can be used
to optimize the adjustment of both your workstation's gamma factor
and/or montior brightness and contrast.
The images:
- bacteriorhodopsin
-
The structure of Bacteriorhodopsin.
Created using the Ribbonjr and Ilabel programs.
- bilayer membrane protein
-
Model of colicin Ia in its membrane-associated state,
prior to insertion into the bilayer.
Demonstrates use of artificial PDB files for special effects.
- boronated porphyrin
-
A boronated saccharide porphyrin structure
showing atoms, bonds, and van der Waals surface.
Demonstrates other capabilities of the Neon and Conic programs.
- crosseye density
-
Custom designed peptide that forms a 4 helix bundle.
Demonstrates creation of cross eye stereo views.
- custom colors
-
Slip-Loop DNA model.
Discusses specifying custom colors for use in images.
- density and helices
-
Bacteriorhodopsin and microscopic and xray density.
Created by using Density delegate to show electron density contours
- depth cue
-
Rat Trypsin versus Bovine Trypsin.
Highlights how to use depthcuing in Neon.
- DNA binding protein
-
Homeodomain protein segment bound to DNA.
Created by mixing Neon "stick" representation
with Conic "sphere" representation.
- label3d
-
Thymidylate Synthase-DHFR complex.
Details how to make a stereo image with stereo labels.
- NMR constraints
-
Shows MidasPlus' basic NMR distance constraint display capabilities.
- paint
-
Alpha Lytic Protease and two potential substrates.
How to use paint programs (if available) for special effects.
- ribbonjr
-
Slip-Loop DNA model.
Shows use of various Ribbonjr options.
- sliced conic
-
Acetylcholine Receptor.
Demonstrates cutting through Conic images to show interiors.
- transparency1
-
DIP-inhibited Trypsin, space filling and stick models.
How to create "semi-transparent" images.
- transparency2
-
HIV-1 Protease substrate comparison.
Created by additional "semi-transparent" image techniques.
- two views ipaste
-
E.coli Bacteriorhodopsin and density.
Created by collating multiple images.
- walleye density
-
As for "crosseye density" image.
Shows how to create wall eye stereo views
gregc@cgl.ucsf.edu / Images Index / June 1995