Principles of Protein Structure Assignment 1996

A Brief Primer on the Use of RasMol Commands

A number of RasMol facilities can be invoked from the menu bar at the top of the display window (or if you are using RasMenu, at the top of the ... window). However, typing in commands at the prompt (RasMol>) offers much more flexibility. For example, load in a PDB file and type 'ribbons on' (or just 'ribbons'). Notice how the effect differs from simply selecting the Ribbons option under Display section of the menu bar.

Note that many commands have optional parameters which specify thicknesses of bonds, atom radius, ribbon width, strand width etc. For example try

wireframe
wireframe 80
wireframe 160

Other commands for rendering the structure in different styles include spacefill, ribbons and strands (again with optional parameters).

Use wireframe off, ribbons off etc to remove these models.

The commands

colour red
colour blue

are self-explanatory; other colouring schemes include

colour chain
colour temperature
colour shapely
colour structure

(The shapely option colours residues by amino acid type.)

Selecting Different Regions of a Structure

The operations described above affect only the parts of the structure currently selected (the default is that all atoms of the structure are selected). This is controlled by the versatile select command.

Use select <expression> where <expression> is, for example helix, sheet, protein, solvent, water, glu, hydrophobic, polar, sulphur, zinc, backbone, sidechain ...etc etc. Try these, and then rendering the selected parts in different styles and colours.

Selecting individual residues and atoms

select ala10 selects residue no. 10 of the structure (assuming it is an alanine). Select multiple residues by separating their numbers with commas, eg:

select ala10, phe12, cys21, gly40

However, the residue names can be omitted:

select 10, 12, 21, 40

Select a range with a dash

select 5-20

If the structure has more than one chain (e.g. 'A' and 'B'), specify the chain by putting it directly after the number e.g.

select ala10A
select ala10A , cys7B

etc. (In fact it is case-insensitive.) Or omit the residue names:

select 10A 7B

etc. Individual atoms may be specified as follows:

select glu10.N
select ile57B.CA

etc. Note that more complex expressions can be constructed by using logical operators, e.g.

select ile57B and sidechain

does not select the backbone atoms of this residue.

The RasMol documentation, including Cammand Reference, is also on the WWW, in the PPS2 hypertree, and also at Brookhaven National Laboratories Structural Biology Department.

Intro to Assignment 1

Last updated 2nd Apr '96