BIRLA INSTITUTE OF SCIENTIFIC RESEARCH
Summer Training: 2016
Summer Training: 2016
Day4: "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.
- 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.
- 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)
- 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.)
- select hydrophobic; color magenta; wireframe 0.4; select not water
- M Display-- Spacefill; M Option-- Slab mode
- 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
- 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).
- 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.
- 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
- 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).
- 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
- 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
- M Option-- Stereo; stereo -5
- M Display-- Wireframe; ssbonds 0.8; color ssbonds yellow
- M Edit-- Select All; M Display-- Backbone; M Colour-- Chain
- set ssbonds backbone
- 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)
- 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 protein and select not protein.
- show information
- show selected
- show sequence
- 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.
- Provides side by side display of the molecule.
- Make sure entire molecule is selected
- Ras MOL>stereo.
|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/off||Atoms 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|