The coordinates of an enzyme inhibitor bound to a domain of calpain is named 'map.pdb'. Here a ball-and-stick figure of the inhibitor will be made in stereo, along with a density map.
The data preparation utility was called:
ribbons-data map
The NameTag is the default 'map'. Click 'Create map.model'. The model-data utility is called, bringing up a sub-panel.
The defaults are fine. Click 'Generate' at the lower left of the form. A message of successful completion should appear. Now click 'Quit and Exit' at the lower right. The sub-panel disappears and a red check should appear saying the model file exists. Now you can add display objects to the model.
Click 'Setup map.atoms' to create atomic spheres. The atoms-data utility is called, bringing up a sub-panel. The defaults create a ball and stick colored by atom type. One change to the defaults is made: a color files is copied over 'map_atoms.color' and edited to make the iodine purple. Click 'Execute' at the lower left of the form. This will create the *.atoms and *.bonds database files, and the primitives as *.sph and *.cyl files. Now click 'Quit and Exit' at the lower right. The subpanel disappears and a red check says the files exist for both atoms and bonds.
A dot surface was made for comparison. Click 'Setup map.ndots' to invoke the ndots-data utility . The default behavior makes use of the *.sph file just created. The defaults are file. Just click 'Execute' and 'Quit' after successful completion.
For the density map 'diff_map.dsn6' (not included as too big), click 'Setup map.texts' to invoked the polys-data utility. The default is for density maps with a 2.0 sigma cutoff. The default map name was set to the file above, and clipping was set for a 7.0 angstrom box around the center (as calculated by model-data). Click 'Execute' and 'Quit' after successful completion.
The density map model is now ready for display.
Click 'Execute Command: ribbons -n map' at the bottom of the form.
The graphics window was made as large as possible. Alt-g (or view menu) was hit to toggle backGround to white. LeftMouse/MiddleMouse to scale/rotate the molecule. Alt-p (or edit menu) was hit to bring up the poly panel. The (default) solid surface was put into line mode and the line width increased. Alt-p closes the poly panel.
The atom panel (Alt-a) & bond panel (Alt-b) were called and complexity increased for a smoother picture. The bonds were scaled smaller. The ndot panel (Alt-n) was used to create large, round dots, with all colors set to deep blue. Alt-2 (view menu -> stereo) puts the display in side-by-side stereo mode. Alt-i (or file) to set image file for save, hit PrintScreen to save the image, and finally Alt-z (or file) to save all the changes as initialization files for the demo. Scaled and sharpened the image with the SGI tool imgworks.
Quit and Exit 'ribbons-data'. To view again: ribbons -n map.