Summer Training Exercises

"Rasmol : Command Line"

Visualization of Protein using RasMol


Rasmol is a computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecule structures.

Getting Started

  • Start Rasmol from your computer's Dektop.

  • This will open two Windows (one Black window, another white command-line window)

  • Commands below preceded by M are best done from the pull-down Menus. Command NOT preceded by M must be typed in the white command-line window. (RasMol has two windows, one black and one white. On windows, the white command-line window starts minimized. look for it on the taskbar. Command with blue colour listed below seprated by semicolons should be typed on separate lines into the white window, pressing Enter after each command.

  • Run RasMol, and do M(enu) File-- Open. Select 1d66.pdb (gal4 transcriptional regulator complexed to DNA).

  • Download ( Save file by Ctrl+S ) 1d66.pdb

  • (The structure will be saved in your download folder). Open RASMOL and select the structure from your download folder.
  1. How many Chains are there?

    • reset; rotate z 90; zoom 150; rotate y 40

    • M(enu) Display-- Backbone, M colours-- Chain
      (Now each chain in different colour. Click on each chain to report its ID letter code)

  2. Is there anything else in this PDB file besides the protein/DNA chains?

    • select hetero; M Display-- Spacefill
      (Now you can see oxygen from water in the X-rayed crystal.)

    • M Colours-- CPK

    • Restrict not water
      (This hides water; Click on what remains to find out what it is.)

  3. What are the hydrophobic aminoacids?

    • select hydrophobic; color magenta; wireframe 0.4; select not water

    • M Display-- Spacefill; M Option-- Slab mode

  4. What holds the CD ions in place?

    • M Display-- Backbone; M Colours--Chain

    • select cd; M Display-- Spacefill; M Colours-- CPK

    • select within(2.6, cd)
      (This selects all atoms within 2.6 Angstroms of the Cd++ ions)

    • M Display-- Spacefill; M Colours-- CPK

    • save script myview1.spt; M File-- Close; script myview1.spt
      (Restore script)

  5. Where are the alpha helices and beta strands?

    • M Edit-- Select all; M Display-- Backbone; M Colours-- Structure
      (This colors alpha helices purple, and beta strands yellow (there aren't any beta strand in 1d66.pdb) Turns appear blue).

  6. How do I find distance between two atoms?

    • M Display-- Spacefill; set picking
      (Now click on two atoms, and watch the report in command line window)

    • set picking monitor
      (Now click on two atoms and watch report at graphic window)

    • color monitor white; set monitor off; monitor off; set picking ident.

  7. How do I see the inside of a molecule?

  8. Don't rotate the molecule with mouse at any time during this sequence.

    • reset; M Edit-- Select All; M Display-- Spacefill; M Colour-- Chain.

    • rotate x 83; zoom 200; M Option-- Hetero Atoms
      (Toggle off waters)

    • select dna; color cpk; M Option-- Slab Mode
      (Toggle on slab mode)

    • slabmode section;
      (Now only cut face is shown)

    • slab 76
      (Now you can see GC base pair).

    • slab 68

  9. How do I keep the DNA from rotating off screen?

    • reset; restrict dna; rotate z 90;
      (Try rotating around the axis of the DNA helix, move the mouse up and down)

    • center selected
      (Now try again and notice the difference).

  10. How do I get multiple representation of the same atoms?

    • restrict :d; M Colours-- CPK
      (:d means all atoms in chain D)

    • M Display-- Backbone, M Display-- Ball & Stick

    • backbone 1.
      (Be sure to include the decimal point after the 1, which make RasMol interpret it as Angstroms)

    • spacefill off; wireframe 0.5; wireframe 0.1; spacefill 0.3; backbone 0.1; zoom 500

  11. How do I label an atom?

    • set picking label
      (Now click on a few atoms)

    • color labels white; label off; set picking ident
      (Click on an atom and notice its own ID number(3rd word in the report). We'll refer to the number as ### in the command below)

    • select atomno = ###; label "My Favorite atom"; label off

  12. How do I see the molecule in stereo?

    • M Option-- Stereo; stereo -5

  13. Where are the disulphide bonds?

    • M Display-- Wireframe; ssbonds 0.8; color ssbonds yellow

    • M Edit-- Select All; M Display-- Backbone; M Colour-- Chain

    • set ssbonds backbone

  14. Where are the hydrogen bonds?

    • M Edit-- Select All; M Display--Backbone; M Colour-- Structure

    • restrict helix; backbone 0; hbonds 0.5; color hbonds white

    • set hbonds backbone; hbonds off; restrict sheet; restrict not (helix or sheet)

  15. Some powerful command with select

    • select single Amino acid----use three letter abbreviation like lue27.
      Example select lue27

    • Amino acid type........... abbreviation like aa type
      Example select asp

    • Entire molecule
      Example select *

    • Chain -select *chain letter
      select *A

    • Select protein and select not protein.

  16. Molecule description with show command.....

    • show information

    • show selected

    • show sequence

  17. Slab mode.......

    • Allows you to look at internal regions of the molecule, by slicing on the z axis.

    • Zero is define as behind the molecule and 100 is defined as in front of the molecule.

    • slab 0-100, example slab 50 cuts at approximately the mid line of the molecule.

  18. Stereo Command..........

    • Provides side by side display of the molecule.

    • Make sure entire molecule is selected

    • Ras MOL>stereo.

  19. On and Off commands..........

wireframe on/off Display wireframe
wireframe 0.2 Display stick bonds of radius 0.2
backbone on/off Display CA backbone only
backbone 0.2 Display CA backbone as sticks of radius 0.2
spacefill on/offAtoms as spacefill spheres
spacefill 1.0 Atoms as spheres of radius 1.0
ribbons on/off Display molecule ribbons
ribbons 1.0 Display molecule ribbons, width 1.0
cartoon on/off Display protein cartoon
dots on/off Display dot-surface about all atoms
dots 10 Display low-density dot-surface
hbonds on/off Display hydrogen bonds
hbonds 0.1 Display hydrogen bonds, radius 0.1
set axes on/off Display coordinate axes
set boundbox on/off         Display bounding box

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