The coordinates of a viral neuraminidase (na) and its inhibitor dana (basically PDB entry 1nnb) was split into separtate files: na.pdb and inhib.pdb. Here a labeled ball-and-stick figure of the inhibitor will be made.
The data preparation utility was called:
ribbons-data inhib
The NameTag is the default 'inhib'. Click 'Create inhib.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 inhib.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. 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.
To make the labels, click 'Setup inhib.texts'. The default behavior makes use of the *.sph file just created. In 'Reformatting Options', the 3rd choice of the RadioBox, atom name only, is chosen. Then click 'Execute' and 'Quit' after successful completion.
The labeled ball-&-stick model is now ready for display.
Click 'Execute Command: ribbons -n inhib' at the bottom of the form.
The graphics window was made about half the size of the screen. Alt-g (or view menu) was hit to toggle backGround to white. LeftMouse to scale up the molecule. The orientation looks good. Alt-t (or edit menu) was hit to bring up the text panel. The overall color was set to black, and the largest font chosen. The overall text translations were set to move the labels off the atom centers. Alt-t closes the text panel.
The atom panel (Alt-a) & bond panel (Alt-b) were called and complexity increased for a smoother picture. Decided on black carbons. Since it is the only green, called the color editor (Alt-c) and adjusted 'green' to shiny black. Decided this was enough for the first tutorial. 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.
Quit and Exit 'ribbons-data'. To view again: ribbons -n inhib