" and " " or " ", " ". "Parameter "canvas" "ribbon" (HELIX (RGB) (Tripos' (acidic (element) (or (positi (prefer) to b (protein or nucleic) and not (refer (the default), the colour is taken from the alpha carbon at each ). When this value is 100 Additional Alchemy All All amino acids are classified as either All nucleotides are either Alpha Amino An a Angstrom Angstroms Angstroms) and 100 (0.4 Angstroms) for turns and random coil. The Apple Atom Atom Expressions Atoms in nucleic acids and proteins are either Backbone Background Bacon's Blue Bond By default Carbon Chain Colour Colour Schemes Colours Command Reference Comparison Operators Currently DSSP Databa David Define Displa Drawing Each Example Expressions Examples: Expression For Gre HBond Hence Hetero High However, Hydrogen Initially, Internal Parameters Introduction Kabsch Kinemage Macintosh Microsoft N-C-C-O Nitrogen Note Number Operators Otherwise, it uses the DSSP algorithm as used by the RasMol PDB Parameters Permited values for the axis parameter are Phe, PostScript Predefined Primitive Expressions Protein RasMol Raster Red, Reference Res Richardson's Rotate SER SSBonds Sander's Sander's DSSP algorithm. By default, RasMol uses the secondary Schemes Script Select Set Solvent Specular Strands Structure Sulphur Syntax: The The RasMol The command The default width of protein alpha helices and beta sheets is 380 (1.52 The difference between the The distinction between this command and the RasMol The width of the ribbon at each position is determined by the optional These This This set contains the This set contains the atoms in the complementary nucleotides This set contains the atoms in those amino acids that tend This set is equivalent to the RasMol atom expression This set is equivalent to the RasMol expression Type "help expression" for more information on RasMol atom expressions. Typically Typing UNIX Use the RasMol predefined sets VMS Val Van Waal's When When running under X Windows, RasMol also recognises colours in the When using RasMol on a UNIX or VMS system this functionality may be Windows Within Expressions X server's colour name database. [0,0, [0,255,0] [0,255,255] [160,32,240] [200,200,200] [230,230,0] [240,0, [255,0,0] [255,0,255] [255,165,0] [255,20 [255,255,0] [255,255,255] `bonds' `default' abbreviat about above accept accessib according acessib achieved by acid acidic acids acids. actual acyclic addition adenosine alchemy algorithm aliphatic all allows along alpha alphabetic also alter altered using the RasMol ambient amino amount and angstroms) anisotropic annotated another any appear appli approp appropriately. approximat arbitrary are are classified as either the set arg, his, lys argument aromatic around as assignment associate assumed atom atom. atoms atoms are classified as either atoms are further classified as either atoms, atoms. author automatically available away axes axis backbone background base basic be been behaviour being below. beta between bindings biomolecular blue bond bonded bonding bondmode bonds boolean both boundbox bounding box brackets brackets. Typing the command bridges buried button by calculat can carbon case cause cell centre chain chang change changed character charge charge/temperature charged classified clipboard closest clutter co-ordinate codes coeffi cofactor colour colour dots potential colour may be given as either a colour name or a comma separated colour ribbon colour scheme colour schemes is that increasing temperature values proceed from blue coloured colouring colours comm comma command command displays the currently loaded protein or nucleic acid as a command e command generates command has been dropped. The only difference is that without a format command is command is similar the the commands command, i.e. the behaviour of command. command. If the current ribbon colour is command. This command is similar to the RasMol command commands commonly communication comparison comple complementary components compose confused connect connected connecti consists constant construct contact contain contained containing contains contents control controlled controls conven corre corresponds cpk crystal crystallograph current currently cursor curves cut-off cyan cyclic cylinder cysteine cystine cytidine dark grey darke data database decimal default default, define defini delete delimited density depend depth-cued der detail determination determine determined determines deuterium differen disable discarded. display displayed distance distinction distinguish disulphide document does donor dot dots dotted drawn driver dropped. each echo effect either electro element elemno enable enclosed equal equivalent error. evaluate example except execut existing exists. exit expansion expression expressions false field file file and the file. files first followed following fontsize for form format forming four from function furthe generate generati give given gives graphic gravity greater green grey group guano has have hbond hbonds helices helix help help colours hence hetero heterogenous high highlights his parameter is similar to the RasMol his, hourglass hydrogen hydrophobic i.e. identi ignore image implementation in the include included in the default set. If both increasing indicat individual inequality information initial input insensitive insight instead integer intended intensity inter interactive internal introduced ions is is synonymous with the is taken from the secondary structure of the protein or a constant value its keywords kinemage label large length. less ligand light line list load loaded local logical lower macromolecul magenta magnification manipulate maximum may mechani medium member menu method middle mode models modify molecule molecule. molecules more mouse move must name names negative neutral non normal not nucleic nucleotide number numeric object objects of of 720 off often one only operat operators opti optional options or or the set orange ordering original orthogonal other out outlines output oxygen packag parallel parameter parameter in the usual RasMol units. By default the width of the ribbon parameter is use parameter is used to modify the `default' behaviour of the RasMol part particularly parts passing percentage perform permissible permit phe, phosphate phosphate backbone of nucleic acids. phosphorous pixels plane plastic point polar polypeptide portion position positive possible potential preced predefined preference and not the actual solvent ac primitive print proceed produc program properties property protein provid purine purple purpose pyrimidine quanta quit radius random range rasmol raster read reco recognise red refers reflection region remain render renumber reports represent representation reproduce require rese resets residue residues respectively rest restrict result ribbon ribbons right rings. rotate rotation running same save scal schematic scheme screen script searches second secondary secondary structure assignment is either from the PDB file or calculated select select all. selected selecting selects separate sequence sequentially ser server's set set axes set background set bondmode set boundbox set display normal set display selected set fontsize set h set hbond set hbonds sidechain set kinemage set m set radius set s set shadow set specular set ssbond set strands set unitcell set vectps set. sets shadow shapely sheet should show show information show sequence show symmetry sidechain similar single size slab slabmode small smooth solid solvent solvent molecules. This set refers to the amino acids some source space spacefill specified specifier specifies specify specpower spectrum specular sphere square ssbonds standard stat stick stored stores strands string structure structure determination given in the PDB file if it exists. subject subsequent such suitable sulphate sulphur supplie support surface symmetry synonymous system table taken temperature tend terminus text than that that display orthogonal co-ordinate axes and the bounding box the the RasMol the current the default their them these this those thymidine time to to red, whereas increasing charge valuse go from red to blue. tra transform translat triple true true, turn turns two type typically under unique unit unitcell units upon use used useful user uses using using the using the DSSP algorithm as used by the value values valuse vari vector vectps view viewpoint water when whereas whether which whil white whole whose width will will give a list of the predefined colour names recognised by RasMol. window wireframe with within without without any parameters is equivalent to without any parameters. When this value is write yellow zero zoom {} {} {} {} {} {} { {}