Ribbons

Ribbons can be run using a menu page options. This will run all the necessary auxillary programs and create all the necessary files behind the scenes. You simply step through and generate the ribbons, atoms and spheres, text, dots, etc. one at a time.

Ribbons needs the following highlighted files in order to display a ribbon image; the remainder are additions to improve or add features to the image:

• name.pdb file of protein atomic coordinates
• name.coord lists the PDB coordinate files used
• name.model gives the point for the center of rotation
• name.ribbons lists the files to be used to generate the ribbons
• name.ss lists residue # and coloring options for ribbons
• name.atoms lists sphere filenames
• name.sph atom spheres, xyz coordinates and atom names
• name.bonds lists cylinder filenames
• name.cyl bond cylinders, xyz coordinates and atom names
• name.texts lists string filenames
• name.str text strings, text and xyz coordinates
• name.ndots lists dot filenames
• name.dot dot coordinates
• name.polys
• name.default lists majority of the display options
• name.matter lists more display options, lighting
• name.orient rotation/translation matrix for display orientation

NOTE

To generate bonds, dots, texts, etc., first one must have generated a sphere file for all of the atoms to be connected with bonds, to be drawn as dots, or to have labels given, etc.

Ribbons tutorial: Alcohol Dehydrogenase (5adh)

If you are in our lab, at unix prompt type:

• If you are in another directory (i.e. you have been working on another tutorial previously) then you need to type cd .. so that you are in your home directory again
• mkdir RibTut01
• cd RibTut01
• cp /sw2/data/Pdb/5adh.pdb 5adh.pdb
• Otherwise the file you need is 5adh.pdb.
• ribbons-data 5adh

This will open up a ribbons menu page with many options.

1. SET-UP ONLY:

• Click on "Create 5adh.model"
• Generate: 5adh.model (results: successful)
• Quit & Exit

2. CREATE RIBBONS AND THEN VIEW FIGURE:

• Click on "Setup 5adh.ribbons"
  • highlight B-factors
  • Execute Command (results: successful)
  • Quit & Exit
• To view: Click on "ribbons -n 5adh"

3. CREATE ATOM SPHERES AND CYLINDERS FOR LIGAND AND VIEW

• Go back to the menu window, with mouse in the figure window type Alt F3.
• Click on "Setup 5adh.atoms"
  • under selection type: resname ADR
  • highlight make bonds too.
  • change filenames: 5adh.sph to 5adh_a.sph and 5adh.cyl to 5adh_a.cyl.
  • Execute Command (results: successful)
  • Quit & Exit
  • Pull the figure window forward again, click on it or type Alt F1.
• select File/ ReRead Data/ Everything

4. CREATE SPHERES AND THEN TEXT FOR LABELS AND VIEW

• A. Go back to the menu window.
• B. Click on "Setup 5adh.text"
  • i. to label the atoms of ADR
    • change filenames: 5adh.sph to 5adh_a.sph
    • 5adh.str to 5adh_a.str
    • highlight the reform option "OH" only.
    • Execute Command (results: successful)
  • ii. to label N-termini
    • change filenames: 5adh.sph to 5adh_t.sph
    • 5adh.str to 5adh_t.str
    • call "atoms-data"
    • change filenames: 5adh.sph to 5adh_t.sph
    • 5adh.cyl to 5adh_t.cyl
    • do not highlight make bonds too.
    • under selection type: resi 1 and name ca
    • Execute Command (results: successful)
    • Quit & Exit
    • highlight the reform option "Y 23" only.
    • Execute Command (results: successful)
    • Edit *.str file
    • if you are not familiar with vi, seek the help of an instructor or see the vi commands in the introduction:
    • follow vi commands to change "S 1" to "N-term"
    • Quit & Exit
• C. Pull the figure window forward again, click on it or type Alt F1.
  • select File/ ReRead Data/ Everything

5. CREATE DOT SURFACES FOR LIGAND (USING PREVIOUSLY GENERATED SPHERE FILE)

• A. Go back to the menu window.
• B. Click on "Setup 5adh.ndots"
  • change filenames: 5adh.sph to 5adh_a.sph
  • Execute Command (results: successful)
  • Quit & Exit
• C. Pull the figure window forward again, click on it or type Alt F1.
  • select File/ ReRead Data/ Everything

6. TO MODIFY THE DISPLAY:

• select Edit/ ...
• for instance, to modify the dot surface:
  • select Edit/ N-dot Control Panel/
  • select Atoms/ pull down menu, then select the list which you are interested in modifying.
  • 1. atom display: highlight on or unhighlight (off)
  • 2. draw style: select round
  • 3. linewidth: select 3
  • 4. overall color:
  • Close Ndot panel.
• for instance, to modify the text size, etc.:
  • select Edit/ Text Control Panel/
  • select strings/ 5adh_a.str and turn off
  • select strings/ 5adh_t.str
  • 1. text font: Helvtca 18
  • 2. X shift -4.0, Y shift 1.5
  • 3. overall color: 11~silver
  • Close Text panel.
• for instance, to modify the ribbon characteristics:
  • The Ribbon Style Panel allows one to change: from solid ribbon to line ribbon, ribbon color, courseness of ribbon (round or square).
  • The Ribbon Nprimitives Panel allows one to change: number of strands in line ribbon, border of ribbons, sidedness of the ribbons, and sampling number (for calculating the ribbon coordinates).
  • The Ribbon Dimensions Panel allows on to change: the dimensions of the ribbons, etc.

7. TO SAVE FIGURE, ADDITIONS AND MODIFIED DISPLAY

• select File/ Save all 3 below/

Ribbon Colors, highlighted under ribbon style panel.

ss = secondary structure

hb = hydrogen bonding potential

B (res, sc, mc) = crystallographic temperature factor (by residue,

by sidechain or by mainchain)

LMB Zoom

MMB Rotation

RMB Translation

one click on the MMB stops the automatic rotation.