Intro to Assignment 1
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 160Other 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.
colour red colour blueare self-explanatory; other colouring schemes include
colour chain colour temperature colour shapely colour structure(The shapely option colours residues by amino acid type.)
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.
select ala10, phe12, cys21, gly40However, the residue names can be omitted:
select 10, 12, 21, 40Select a range with a dash
select 5-20If 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 , cys7Betc. (In fact it is case-insensitive.) Or omit the residue names:
select 10A 7Betc. Individual atoms may be specified as follows:
select glu10.N select ile57B.CAetc. Note that more complex expressions can be constructed by using logical operators, e.g.
select ile57B and sidechaindoes 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.
Last updated 2nd Apr '96