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:

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:

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.
Thymidylate Synthase-DHFR complex. Details how to make a stereo image with stereo labels.
NMR constraints
Shows MidasPlus' basic NMR distance constraint display capabilities.
Alpha Lytic Protease and two potential substrates. How to use paint programs (if available) for special effects.
Slip-Loop DNA model. Shows use of various Ribbonjr options.
sliced conic
Acetylcholine Receptor. Demonstrates cutting through Conic images to show interiors.
DIP-inhibited Trypsin, space filling and stick models. How to create "semi-transparent" images.
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