NAME

heme − depthcued display of the Cytochrome P450 protein molecule

SYNOPSIS

/usr/people/mexdemos/heme

DESCRIPTION

Dr. Tom Poulos and Prof. Joseph Kraut of the University of California at San Diego have constructed a computer model of the Cytochrome P450 molecule to aid in their research into the structure of this enzyme. Computer graphics help in comparing electron density maps to the proposed protein structure by moving the hypothetical structure into regions of high electron density.  Proximity of atoms provides information regarding chemical interaction. 

heme displays the Cytochrome protein with control of viewing transformations via pop-up menu selections. Also, display of various parts of the protein molecule can be toggled on and off.  When all portions are displayed, the molecular model is comprised of 1022 points and 549 vectors. 

Pop up the menu by holding down the CENTER mouse button. Menu selections are are toggled by placing the cursor atop the menu selection and pressing the LEFT mouse button. The menu disappears when the CENTER mouse button is released. 

Left Function
Menu
5Amino acids that interact with the heme group.
4 Backbone of P450, connecting alpha-carbons
of amino acid subunits.
3Electron density contour around the iron atom.        
2 Van der Waals surface of the heme group.
1 The heme group, the subunit which accepts
and donates electrons.

The right menu is a series of glyphs which specify the transformations affecting the molecule.  From top to bottom, the first button turns depth-cueing on and off.  The next six menu buttons rotate the molecule around the x, y and z axes.  The next six menu buttons translate the molecule in the x, y and z directions.  The next two menu buttons scale the molecule (larger or smaller).  The next to last button is the bungalow (house) icon, which resets the initial position of the molecule.  The house represents returning to home.  The stop sign is, of course, the exit. 

The depth-cueing uses either 32 or 16 intensities per color, depending upon the number of available planes of image memory.  The initial display is designed to emphasize the central structure of the model.  If the model is translated far enough away to be completely visible, the depth- cueing will render it virtually invisible.  To see the whole model, scale it down and translate it forward until the perspective, Z-clipping, and depth-cueing give an attractive image. 

DIAL AND BUTTON BOX OPERATION

If a dial and button box is connected to the IRIS, it can be used to control the molecule.  Typing k (which stands for knobs) activates the dial and button box as the input device.  Refer to the dials and buttons by the names in this chart:

32 Buttons
SW0SW1SW2SW3
SW4SW5SW6SW7SW8SW9
SW10SW11SW12SW13SW14SW15
SW16SW17SW18SW19SW20SW21
SW22SW23SW24SW25SW26SW27
SW28SW29SW30SW31
 8 DIALS
DIAL6DIAL7
DIAL4DIAL5
DIAL2DIAL3
DIAL0DIAL1

When the dial and button box is selected as the new input device, all current transformations (rotations, translations, and scaling) stop.  The dials and buttons take over the functions originally found on the pop-up menu:

Button Function
SW0Depth-cueing, on and off
SW1Return to home position (bungalow icon equivalent)
SW2Unused
SW3Exit the program
SW4 The heme group, the subunit which accepts
and donates electrons.
SW5 Van der Waals surface of the heme group.
SW6Electron density contour around the iron atom.
SW7 Backbone of P450, connecting alpha-carbons
of amino acid subunits.
SW8Amino acids that interact with the heme group.
SW9-SW31 are unused
Dials Functions
DIAL0enlarge and shrink (scale) molecule
DIAL1unused
DIAL2,4,6rotate molecule around z, y and x axes (respectively)
DIAL3,5,7translate molecule in z, y and x
directions (respectively)

Type the k key again to restore the mouse, with its pop-up menu, as the input device. 

WINDOW MANAGER

The heme executable can only run under the window manager.  A special option with the window manager version of heme continues the motion of the molecule, even when the window is detached.  This motion option is turned on and off by typing m. 

HARDWARE CONFIGURATION

A minimum configuration of 20 bitplanes of image memory is required to run heme. 
 

Version 2.5  —  April 22, 1987