This is the alpha release of ribbons for the PC. There is only one executable program - all the utilities have been incorporated. The executable should be compatible with any previously prepared data.
The program has a very different interface, programmed by Jun Dai. Any comments/suggestions should be mailed to mike.carson@cmc.uab.edu
1) get ready
Create a new directory and copy over a PDB file.
The program creates all auxilliary data in the same directory as the
PDB file.
Suggest you use a single-chain small protein, like
~ribbons/data/ubiq.pdb, for your demo (at least that's what i did).
2) create *.model
Double-click the Ribbons.exe icon to start the program,
It should fill the screen with a large black viewing area on the left, and
a data management subwindow on the right.
Select 'New' under the 'File' menu. A dialog box pops up.
Type in a name for the model, then click 'Open' to browse for a PDB
file.
Then click 'OK'. Axes appear in the graphics window, and a list with
your model name appears in the data management window.
3) create data files
The data management window lists the types of objects standard in
ribbons.
Let's assume you want to make an actual ribbon drawing:
Click 'RIBBON'. Click with RightMouse to bring up the context-sensitive
menu.
Enter a name tag for the domain. Open the PDB file.
You still must have only all amino acids or all nucleic acids for a
ribbon.
If this is true, just click 'OK'. A ribbon model of the entire file
appears.
If you must use only a part of the file, click the 'Derive' button.
This allows you to save a subset of atoms to a new PDB file for the
ribbon.
As an example, let's add all Histidine atoms as spheres.
Click 'ATOM' with the RightMouse. Set the domain name to 'his'.
Open the same PDB file. Then click the 'Derive' button.
Change the name of the new PDB file if you like, eg, to 'his.pdb' from
default.
Select 'HIS' under 'Res.N'. Then click 'Res.N'. It should beep, then
'Close'.
This should return you to the ATOM menu with a PDB file of only
Histidines.
Click OK and the atomic spheres should be added to the display.
The other primitives are added in much the same way.
4) manipulate the model
Hold down the LeftMouse and move in the graphics window for rotation.
Hold down the RightMouse in the graphics window to select another mode,
such as 'Scale'.
The cursor should change to indicate the state.
There have been many little icons derived as shortcuts to editor panels.
The panels have a different look, but should accomplish the same ends.
What was called the 'Edit' main menu is now called 'Style'.
To open the 'Atom Panel', either select 'Atom' from 'Style' on menubar,
or select the cute "atomic" icon to adjust radii, etc.