RASMOL(1) User Commands RASMOL(1) NNNNAAAAMMMMEEEE rasmol - Molecular Graphics Visualisation Tool v2.5 SSSSYYYYNNNNOOOOPPPPSSSSIIIISSSS rrrraaaassssmmmmoooollll [---- nnnnooooddddiiiippppllllaaaayyyy] [[ ---- _f_o_r_m_a_t ] _f_i_l_e_n_a_m_e] [ ---- ssssccccrrrriiiipppptttt _s_c_r_i_p_t_f_i_l_e] FFFFOOOORRRRMMMMAAAATTTTSSSS ----ppppddddbbbb Brookhaven Protein Databank ----mmmmddddllll MDL's MOL File Format ----mmmmoooollll2222 Tripos' Sybyl MOL2 Format ----xxxxyyyyzzzz MSC's XYZ (XMol) Format ----aaaallllcccchhhheeeemmmmyyyy Alchemy File Format ----cccchhhhaaaarrrrmmmmmmmm CHARMm File Format DDDDEEEESSSSCCCCRRRRIIIIPPPPTTTTIIIIOOOONNNN RasMol2 is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images. RasMol runs on Microsoft Windows, Apple Macintosh, UNIX and VMS systems. The UNIX and VMS systems require an 8, 24 or 32 bit colour X Windows display (X11R4 or later). The program reads in a molecule co-ordinate file and interactively displays the molecule on the screen in a variety of colour schemes and molecule representations. Currently available representa- tions include depth-cued wireframes, 'Dreiding' sticks, spa- cefilling (CPK) spheres, ball and stick, solid and strand biomolecular ribbons, atom labels and dot surfaces. CCCCOOOOMMMMMMMMAAAANNNNDDDDSSSS RasMol allows the execution of interactive commands typed at the RRRRaaaassssMMMMoooollll>>>> prompt in the terminal window. Each command must be given on a separate line. Keywords are case insensitive and may be entered in either upper or lower case letters. All whitespace characters are ignored except to separate keywords and their arguments. The commands/keywords currently recognised by RasMol are given below. BBBBaaaacccckkkkbbbboooonnnneeee The RasMol bbbbaaaacccckkkkbbbboooonnnneeee command permits the representation of a polypeptide backbone as a series of bonds connect- ing the adjacent alpha carbons of each amino acid in a chain. The display of these backbone `bonds' is turned on and off by the command paramater the same as the wwwwiiiirrrreeeeffffrrrraaaammmmeeee command. The command bbbbaaaacccckkkkbbbboooonnnneeee ooooffffffff turns off Sun Microsystems Last change: October 1994 1 RASMOL(1) User Commands RASMOL(1) the selected `bonds', and bbbbaaaacccckkkkbbbboooonnnneeee oooonnnn or with a number turns them on. The number can be used to specify the cylinder radius of the representation in either angstrom or rasmol units. A parameter value of 500 (2.0 angstroms) or above results in a "Parameter value too large" error. Backbone objects may be coloured using the RasMol ccccoooolllloooouuuurrrr bbbbaaaacccckkkkbbbboooonnnneeee command. BBBBaaaacccckkkkggggrrrroooouuuunnnndddd The RasMol bbbbaaaacccckkkkggggrrrroooouuuunnnndddd command is used to set the colour of the "canvas" background. The colour may be given as either a colour name or a comma separated triple of Red, Green and Blue (RGB) components enclosed in square brackets. Typing the command hhhheeeellllpppp ccccoooolllloooouuuurrrrssss will give a list of the predefined colour names recognised by RasMol. When running under X Windows, RasMol also recognises colours in the X server's colour name data- base. The bbbbaaaacccckkkkggggrrrroooouuuunnnndddd command is synonymous with the RasMol sssseeeetttt bbbbaaaacccckkkkggggrrrroooouuuunnnndddd command. CCCCeeeennnnttttrrrreeee The RasMol cccceeeennnnttttrrrreeee command defines the point about which the rrrroooottttaaaatttteeee command and the scroll bars rotate the current molecule. Without a parameter the centre com- mand resets the centre of rotation to be the centre of gravity of the molecule. If an atom expression is specified, RasMol rotates the molecule about the centre of gravity of the set of atoms specified by the expres- sion. Hence, if a single atom is specified by the expression, that atom will remain `stationary' during rotations. Type hhhheeeellllpppp eeeexxxxpppprrrreeeessssssssiiiioooonnnn for more information on RasMol atom expressions. CCCClllliiiippppbbbbooooaaaarrrrdddd The RasMol cccclllliiiippppbbbbooooaaaarrrrdddd command places a copy of the currently displayed image on the local graphics `clip- board'. Note: this command is not yet supported on UNIX or VMS machines. It is intended to make transfering images between applications easier under Microsoft Win- dows or on an Apple Macintosh. When using RasMol on a UNIX or VMS system this func- tionality may be achieved by generating a raster image in a format that can be read by the receiving program using the RasMol wwwwrrrriiiitttteeee command. Sun Microsystems Last change: October 1994 2 RASMOL(1) User Commands RASMOL(1) CCCCoooolllloooouuuurrrr Colour the atoms (or other objects) of the selected region. The colour may be given as either a colour name or a comma separated triple of Red, Green and Blue (RGB) components enclosed in square brackets. Typing the command hhhheeeellllpppp ccccoooolllloooouuuurrrrssss will give a list of all the predefined colour names recognised by RasMol. Allowed objects are aaaattttoooommmmssss,,,, bbbboooonnnnddddssss,,,, bbbbaaaacccckkkkbbbboooonnnneeee,,,, rrrriiiibbbbbbbboooonnnnssss llllaaaabbbbeeeellllssss ddddoooottttssss,,,, hhhhbbbboooonnnnddddssss,,,, and ssssssssbbbboooonnnnddddssss.... If no object is specified, the default keyword aaaattttoooommmm is assumed. Some colour schemes are defined for certain object types. The colour scheme nnnnoooonnnneeee can be applied all objects accept atoms and dots, stating that the selected objects have no colour of their own, but use the colour of their associated atoms (i.e. the atoms they con- nect). AAAAttttoooommmm objects can also be coloured by ccccppppkkkk,,,, aaaammmmiiiinnnnoooo,,,, cccchhhhaaaaiiiinnnn,,,, ggggrrrroooouuuupppp,,,, sssshhhhaaaappppeeeellllyyyy,,,, ssssttttrrrruuuuccccttttuuuurrrreeee,,,, tttteeeemmmmppppeeeerrrraaaattttuuuurrrreeee cccchhhhaaaarrrrggggeeee and uuuusssseeeerrrr.... HHHHyyyyddddrrrrooooggggeeeennnn bbbboooonnnnddddssss ccccaaaannnn aaaallllssssoooo bbbbeeee ttttyyyyppppeeee and dot surfaces can also be coloured by eeeelllleeeeccccttttrrrroooossssttttaaaattttiiiicccc ppppooootttteeeennnnttttiiiiaaaallll.... For more information type hhhheeeellllpppp ccccoooolllloooouuuurrrr <<<>>>.... CCCCoooonnnnnnnneeeecccctttt The RasMol ccccoooonnnnnnnneeeecccctttt command is used to force RasMol to (re)calculate the connectivity of the current molecule. If the original input file contained connectivity information, this is discarded. The command ccccoooonnnnnnnneeeecccctttt ffffaaaallllsssseeee uses an extremely fast heuristic algorithmm that is suitable for determing bonding in large bio- molecules such as proteins and nucleic acids. The com- mand ccccoooonnnnnnnneeeecccctttt ttttrrrruuuueeee uses a slower more accurate algorithm based upon covalent radii that is more suitable for small molecules containing inorganic elements or strained rings. If no parameters are given, RasMol determines which algorithm to use based on the number of atoms in the file. Greater than 255 atoms causes RasMol to use the faster implementation. This is the method used to determine bonding, if necessary, when a molecule is first read in using the llllooooaaaadddd command. DDDDeeeeffffiiiinnnneeee The RasMol ddddeeeeffffiiiinnnneeee command allows the user to associate an arbitrary set of atoms with a unique identifier. This allows the definition of user-defined sets. These sets are declared statically, i.e. once defined the contents of the set do not change, even if the expres- sion defining them depends on the current transforma- tion and representation of the molecule. Sun Microsystems Last change: October 1994 3 RASMOL(1) User Commands RASMOL(1) DDDDoooottttssss The RasMol ddddoooottttssss command is used to generate a Van der Waal's dot surface around the currently selected atoms. Dot surfaces display regularly spaced points on a sphere of Van der Waals' radius about each selected atom. Dots that would are `buried' within the Van der Waal's radius of any other atom (selected or not) are not displayed. The command ddddoooottttssss oooonnnn deletes any exist- ing dot surface and generates a dots surface around the currently selected atom set with a default dot density of 100. The command ddddoooottttssss ooooffffffff deletes any existing dot surface. The dot density may be specified by providing a numeric parameter between 1 and 1000. This value approximately corresponds to the number of dots on the surface of a medium sized atom. By default, the colour of each point on a dot surface is the colour of it's closest atom at the time the sur- face is generated. The colour of the whole dot surface may be changed using the ccccoooolllloooouuuurrrr ddddoooottttssss command. EEEEcccchhhhoooo The RasMol eeeecccchhhhoooo command is used to display a message in the RasMol command/terminal window. The string parame- ter may optionally be delimited in double quote charac- ters. If no parameter is specified, the eeeecccchhhhoooo command displays a blank line. This command is particularly useful for displaying text from within a RasMol ssssccccrrrriiiipppptttt file. HHHHBBBBoooonnnnddddssss The RasMol hhhhbbbboooonnnndddd command is used to represent the hydrogen bonding of the protein molecule's backbone. This information is useful in assessing the protein's secondary structure. Hydrogen bonds are represented as either dotted lines or cylinders between the donor and acceptor residues. The first time the hhhhbbbboooonnnndddd command is used, the program searches the structure of the molecule to find hydrogen bonded residues and reports the number of bonds to the user. The command hhhhbbbboooonnnnddddssss oooonnnn displays the selected `bonds' as dotted lines, and the hhhhbbbboooonnnnddddssss ooooffffffff turns off their display. The colour of hbond objects may be changed by the ccccoooolllloooouuuurrrr hhhhbbbboooonnnndddd command. Initially, each hydrogen bond has the colours of its connected atoms. By default the dotted lines are drawn between the accepting oxygen and the donating nitrogen. By using the sssseeeetttt hhhhbbbboooonnnnddddssss command the alpha carbon positions of the appropriate residues may be used instead. This is especially useful when examining proteins in backbone representation. Sun Microsystems Last change: October 1994 4 RASMOL(1) User Commands RASMOL(1) HHHHeeeellllpppp The RasMol hhhheeeellllpppp command provides on-line help on the given topic. LLLLaaaabbbbeeeellll The RasMol llllaaaabbbbeeeellll command allows an arbitrary formatted text string to be associated with each currently selected atom. This string may contain embedded `expansion specifiers' which display properties of the atom being labelled. An expansion specifier consists of a `%' character followed by a single alphabetic charac- ter specifying the property to be displayed. An actual '%' character may be displayed by using the expansion specifier `%%'. Atom labelling for the currently selected atoms may be turned off with the command llllaaaabbbbeeeellll ooooffffffff.... By default, if no string is given as a parameter RasMol uses labels appropriate for the current molecule. The colour of each label may be changed using the ccccoooolllloooouuuurrrr llllaaaabbbbeeeellll command. By default, each label is drawn in the same colour as the atom to which it is attached. The size of the displayed text may be changed using the sssseeeetttt ffffoooonnnnttttssssiiiizzzzeeee command. LLLLooooaaaadddd Load a molecule co-ordinate file into RasMol2. Valid molecule file formats are ppppddddbbbb (Brookhaven Protein Data- bank), mmmmddddllll (Molecular Design Limited's MOL file for- mat), aaaallllcccchhhheeeemmmmyyyy (Tripos' Alchemy file format), mmmmoooollll2222 (Tri- pos' Sybyl Mol2 file format), cccchhhhaaaarrrrmmmmmmmm (CHARMm file for- mat) or xxxxyyyyzzzz (MSC's XMol XYZ file format). If no file format is specified, ppppddddbbbb is assumed by default. Only a single molecule may be loaded at a time. To delete a molecule prior to loading another use the RasMol zzzzaaaapppp command. The llllooooaaaadddd command selects all the atoms in the molecule, centres it on the screen and renders it as a CPK coloured wireframe model. If the molecule contains no bonds (i.e. contains only alpha carbons), it is drawn as an alpha carbon backbone. If the file specifies less bonds than atoms, RasMol determines connectivity using the ccccoooonnnnnnnneeeecccctttt command. PPPPrrrriiiinnnntttt The RasMol pppprrrriiiinnnntttt command sends the currently displayed image to the local default printer using the operating system's native printer driver. Note: this command is not yet supported under UNIX or VMS. It is intended to Sun Microsystems Last change: October 1994 5 RASMOL(1) User Commands RASMOL(1) take advantage of Microsoft Windows and Apple Macintosh printer drivers. For example, allowing images to be printed directly on a dot matrix printer. When using RasMol on a UNIX or VMS system this func- tionality may be achieved by either generating a PostScript file using the RasMol wwwwrrrriiiitttteeee ppppssss or wwwwrrrriiiitttteeee vvvveeeeccccttttppppssss commands and printing that or generating a ras- ter image file and using a utility to dump that to the local printer. QQQQuuuuiiiitttt Exit from the RasMol program. The RasMol commands eeeexxxxiiiitttt and qqqquuuuiiiitttt are synonymous. RRRReeeennnnuuuummmmbbbbeeeerrrr The RasMol rrrreeeennnnuuuummmmbbbbeeeerrrr command sequentially numbers the residues in a macromolecular chain. The optional parameter specifies the value of the first residue in the sequence. By default, this value is one. For pro- teins, each amino acid is numbered consecutively from the N terminus to the C terminus. For nucleic acids, each base is numbered from the 5' terminus to 3' ter- minus. All chains in the current database are renum- bered and gaps in the original sequence are ignored. The starting value for numbering may be negative. RRRReeeesssseeeetttt The RasMol rrrreeeesssseeeetttt command restores the original viewing transformation and centre of rotation. The scale is set to it default value, zzzzoooooooommmm 111100000000,,,, the centre of rotation is set to the geometric centre of the currently loaded molecule, cccceeeennnnttttrrrreeee aaaallllllll,,,, this centre is translated to the middle of the screen and the viewpoint set to the default orientation. This command should not be mistaken for the RasMol zzzzaaaapppp command which deletes the currently stored molecule, returning the program to its initial state. RRRReeeessssttttrrrriiiicccctttt The RasMol rrrreeeessssttttrrrriiiicccctttt command both defines the currently selected region of the molecule and disables the representation of (most of) those parts of the molecule no longer selected. All subsequent RasMol commands that modify a molecule's colour or representation effect only the currently selected region. The parame- ter of a rrrreeeessssttttrrrriiiicccctttt command is a RasMol atom expression that is evaluated for every atom of the current Sun Microsystems Last change: October 1994 6 RASMOL(1) User Commands RASMOL(1) molecule. This command is very similar to the RasMol sssseeeelllleeeecccctttt command, except restrict disables the wwwwiiiirrrreeeeffffrrrraaaammmmeeee,,,, ssssppppaaaacccceeeeffffiiiillllllll and bbbbaaaacccckkkkbbbboooonnnneeee representations in the non- selected region. Type "help expression" for more information on RasMol atom expressions. RRRRiiiibbbbbbbboooonnnnssss The RasMol rrrriiiibbbbbbbboooonnnnssss command displays the currently loaded protein or nucleic acid as a smooth solid "rib- bon" surface passing along the backbone of the protein. The ribbon is drawn between each amino acid whose alpha carbon is currently selected. The colour of the ribbon is changed by the RasMol ccccoooolllloooouuuurrrr rrrriiiibbbbbbbboooonnnn command. If the current ribbon colour is nnnnoooonnnneeee (the default), the colour is taken from the alpha carbon at each position along its length. The width of the ribbon at each position is determined by the optional parameter in the usual RasMol units. By default the width of the ribbon is taken from the secondary structure of the protein or a constant value of 720 (2.88 Angstroms) for nucleic acids. The default width of protein alpha helices and beta sheets is 380 (1.52 Angstroms) and 100 (0.4 Angstroms) for turns and random coil. The secondary structure assignment is either from the PDB file or calculated using the DSSP algorithm as used by the ssssttttrrrruuuuccccttttuuuurrrreeee command. This com- mand is similar to the RasMol command ssssttttrrrraaaannnnddddssss which renders the biomolecular ribbon as parallel depth-cued curves. RRRRoooottttaaaatttteeee Rotate the molecule about the specified axis. Permited values for the axis parameter are "x", "y" and "z". The integer parameter states the angle in degrees for the structure to be rotated. For the X and Y axes, positive values move the closest point up and right, and negative values move it down and left respectively. For the Z axis, a positive rotation acts clockwise and a negative angle anti-clockwise. SSSSaaaavvvveeee Save the currently selected set of atoms in either a Brookhaven Protein Database (PDB) or Alchemy(tm) format file. The distinction between this command and the RasMol wwwwrrrriiiitttteeee command has been dropped. The only differ- ence is that without a format specifier the ssssaaaavvvveeee com- mand generates a PPPPDDDDBBBB file and the wwwwrrrriiiitttteeee command Sun Microsystems Last change: October 1994 7 RASMOL(1) User Commands RASMOL(1) generates a GGGGIIIIFFFF image. SSSSccccrrrriiiipppptttt The RasMol ssssccccrrrriiiipppptttt command reads a set of RasMol com- mands sequentially from a text file and executes them. This allows sequences of commonly used commands to be stored and performed by single command. A RasMol script file may contain a further script command up to a max- imum "depth" of 10, allowing compilicated sequences of actions to be executed. RasMol ignores all characters after the first '#' character on each line allowing the scripts to be annotated. Script files are often also annotated using the RasMol eeeecccchhhhoooo command. The most common way to generate a RasMol script file is to use the wwwwrrrriiiitttteeee ssssccccrrrriiiipppptttt or wwwwrrrriiiitttteeee rrrraaaassssmmmmoooollll commands to output the sequence of commands that are needed to regenerate the current view, representation and colour- ing of the currently displayed molecule. The RasMol command ssssoooouuuurrrrcccceeee is synonymous with the ssssccccrrrriiiipppptttt command. SSSSeeeelllleeeecccctttt Define the currently selected region of the molecule. All subsequent RasMol commands that manipulate a molecule or modify its colour or representation, only effects the currently selected region. The parameter of a sssseeeelllleeeecccctttt command is a RasMol expression that is evaluated for every atom of the current molecule. The currently selected (active) region of the molecule are those atoms that cause the expression to evaluate true. To select the whole molecule use the RasMol command sssseeeelllleeeecccctttt aaaallllllll.... The behaviour of the sssseeeelllleeeecccctttt command without any parameters is determined by the RasMol hhhheeeetttteeeerrrroooo and hhhhyyyyddddrrrrooooggggeeeennnn parameters. Type "help expression" for more information on RasMol atom expressions. SSSSeeeetttt The RasMol sssseeeetttt command allows the user to alter various internal program parameters such as those controlling rendering options. Each parameter has its own set or permissible parameter options. Typically, ommiting the paramter option resets that parameter to its default value. A list of valid parameter names is given below. SSSShhhhoooowwww The RasMol sssshhhhoooowwww command display details of the status Sun Microsystems Last change: October 1994 8 RASMOL(1) User Commands RASMOL(1) of the currently loaded molecule. The command sssshhhhoooowwww iiiinnnnffffoooorrrrmmmmaaaattttiiiioooonnnn lists the molecule's name, classification, PDB code and the number of atoms, chains, groups it contains. If hydrogen bonding, disulphide bridges or secondary structure have been determined, the number of hbonds, ssbonds, helices, ladders and turns are also displayed respectively. The command sssshhhhoooowwww sssseeeeqqqquuuueeeennnncccceeee lists the residues that compose each chain of the molecule. SSSSllllaaaabbbb The RasMol ssssllllaaaabbbb command enables, disables or positions the z-clipping plane of the molecule. The program only draws those portions of the molecule that are further from the viewer than the slabbing plane. Values range from zero at the very back of the molecule to 100 which is completely in front of the molecule. Intermediate values determine the percentage of the molecule to be drawn. SSSSppppaaaacccceeeeffffiiiillllllll The RasMol ssssppppaaaacccceeeeffffiiiillllllll command is used to represent all of the currently selected atoms as solid spheres. This command is used to produce both union-of-spheres and ball-and-stick models of a molecule. The command, ssssppppaaaa---- cccceeeeffffiiiillllllllllll ttttrrrruuuueeee,,,, the default, represents each atom as a sphere of Van der Waals radius. The command ssssppppaaaacccceeeeffffiiiillllllll ooooffffffff turns off the representation of the selected atom as spheres. A sphere radius may be specified as an integer in RasMol units (1/250th Angstrom) or a value containing a decimal point. A value of 500 (2.0 Angstroms) or greater results in a "Parameter value too large" error. The tttteeeemmmmppppeeeerrrraaaattttuuuurrrreeee option sets the radius of each sphere to the value stored in its temperature field. Zero or negative values causes have no effect and values greater than 2.0 are truncated to 2. The uuuusssseeeerrrr option allows the radius of each spheres to be specified by additional lines in the molecule's PDB file using Ras- ter 3D's COLOR record extension. The RasMol command ccccppppkkkk is synonymous with the ssssppppaaaacccceeeeffffiiiillllllll command. SSSSSSSSBBBBoooonnnnddddssss The RasMol ssssssssbbbboooonnnnddddssss command is used to represent the disulphide bridges of the protein molecule as either dotted lines or cylinders between the connected cys- teines. The first time that the ssssssssbbbboooonnnnddddssss command is used, the program searches the structure of the protein Sun Microsystems Last change: October 1994 9 RASMOL(1) User Commands RASMOL(1) to find half-cysteine pairs (cysteines whose sulphurs are within 3 angstroms of each other) and reports the number of bridges to the user. The command ssssssssbbbboooonnnnddddssss oooonnnn displays the selected `bonds' as dotted lines, and the command ssssssssbbbboooonnnnddddssss ooooffffffff disables the display of ssbonds in the currently selected area. Selection of disulphide bridges is identical to normal bonds, and may be adjusted using the RasMol sssseeeetttt bbbboooonnnnddddmmmmooooddddeeee command. The colour of disulphide bonds may be changed using the ccccoooolllloooouuuurrrr ssssssssbbbboooonnnnddddssss command. By default, each disulphide bond has the colours of its connected atoms. By default disulphide bonds are drawn between the sul- phur atoms within the cysteine groups. By using the sssseeeetttt ssssssssbbbboooonnnnddddssss command the position of the cysteine's alpha carbons may be used instead. SSSSttttrrrraaaannnnddddssss The RasMol ssssttttrrrraaaannnnddddssss command displays the currently loaded protein or nucleic acid as a smooth "ribbon" of depth-cued curves passing along the backbone of the protein. The ribbon is composed of a number of strands that run parallel to one another along the peptide plane of each residue. The ribbon is drawn between each amino acid whose alpha carbon is currently selected. The colour of the ribbon is changed by the RasMol ccccoooolllloooouuuurrrr rrrriiiibbbbbbbboooonnnn command. If the current ribbon colour is nnnnoooonnnneeee (the default), the colour is taken from the alpha carbon at each position along its length. The colour of the central and outermost strands may be coloured independently using the ccccoooolllloooouuuurrrr rrrriiiibbbbbbbboooonnnn1111 and ccccoooolllloooouuuurrrr rrrriiiibbbb---- bbbboooonnnn2222 commands respectively. The number of strands in the ribbon may be altered using the RasMol sssseeeetttt ssssttttrrrraaaannnnddddssss command. The width of the ribbon at each position is determined by the optional parameter in the usual RasMol units. By default the width of the ribbon is taken from the secondary structure of the protein or a constant value of 720 for nucleic acids (which produces a ribbon 2.88 Angstroms wide). The default width of protein alpha helices and beta sheets is 380 (1.52 Angstroms) and 100 (0.4 Angstroms) for turns and random coil. The secon- dary structure assignment is either from the PDB file or calculated using the DSSP algorithm as used by the ssssttttrrrruuuuccccttttuuuurrrreeee command. This command is similar to the RasMol command rrrriiiibbbbbbbboooonnnnssss which renders the biomolecular ribbon as a smooth shaded surface. SSSSttttrrrruuuuccccttttuuuurrrreeee Sun Microsystems Last change: October 1994 10 RASMOL(1) User Commands RASMOL(1) The RasMol ssssttttrrrruuuuccccttttuuuurrrreeee command calculates secondary structure assignments for the currently loaded protein. If the original PDB file contained structural assign- ment records (HELIX and SHEET) these are discarded. Initially, the hydrogen bonds of the current molecule are found, if this hasn't been done already. The secon- dary structure is the determined using Kabsch and Sander's DSSP algorithm. Once finished the program reports the number of helices, strands and turns found. TTTTrrrraaaannnnssssllllaaaatttteeee The RasMol ttttrrrraaaannnnssssllllaaaatttteeee command moves the position of the centre of the molecule on the screen. The axis parame- ter specifies along which axis the molecule is to be moved and the integer parameter specifies the absolute position of the molecule centre from the middle of the screen. Permited values for the axis parameter are "x", "y" and "z". Displacement values must be between -100 and 100 which correspond to moving the current molecule just off the screen. A positive "x" displace- ment moves the molecule to the right, and a positive "y" displacement moves the molecule down the screen. The pair of commands ttttrrrraaaannnnssssllllaaaatttteeee xxxx 0000 and ttttrrrraaaannnnssssllllaaaatttteeee yyyy 0000 centres the molecule on the screen. WWWWiiiirrrreeeeffffrrrraaaammmmeeee The RasMol wwwwiiiirrrreeeeffffrrrraaaammmmeeee command represents each bond within the selected region of the molecule as either a cylinder, a line or depth-cued vector. The display of bonds as depth-cued vectors (drawn darker the further away from the viewer) is turned on by the command wwwwiiiirrrreeeeffffrrrraaaammmmeeee or wwwwiiiirrrreeeeffffrrrraaaammmmeeee oooonnnn.... The selected bonds are displayed as cylinders by specifying a radius either as an integer in RasMol units or containing a decimal point as a value in Angstroms. A parameter value of 500 (2.0 angstroms) or above results in an "Parameter value too large" error. Bonds may be coloured using the ccccoooolllloooouuuurrrr bbbboooonnnnddddssss command. WWWWrrrriiiitttteeee Write the current image to a file in a standard raster format. Currently supported image file formats include ggggiiiiffff (Compuserve GIF), ppppppppmmmm (Portable Pixmap), rrrraaaassss (Sun rasterfile), ppppssss and eeeeppppssssffff (Encapsulated PostScript), mmmmoooonnnnooooppppssss (Monochrome Encapsulated PostScript), bbbbmmmmpppp (Microsoft bitmap) and ppppiiiicccctttt (Apple PICT). The wwwwrrrriiiitttteeee command may also be used to generate command scripts for other graphics programs. The format ssssccccrrrriiiipppptttt writes out a file containing the RasMol ssssccccrrrriiiipppptttt commands to Sun Microsystems Last change: October 1994 11 RASMOL(1) User Commands RASMOL(1) reproduce the current image. The format mmmmoooollllssssccccrrrriiiipppptttt writes out the commands required to render the current view of the molecule as ribbons in Per Kraulis' Mol- script program and the format kkkkiiiinnnneeeemmmmaaaaggggeeee the commands for David Richardson's program Mage. The distinction between this command and the RasMol ssssaaaavvvveeee command has been dropped. The only difference is that without a format specifier the ssssaaaavvvveeee command gen- erates a PPPPDDDDBBBB file and the wwwwrrrriiiitttteeee command generates a GGGGIIIIFFFF image. ZZZZaaaapppp Deletes the contents of the current database and resets parameter variables to their initial default state. ZZZZoooooooommmm Change the magnification of the currently displayed image. Boolean parameters either magnify or reset the scale of current molecule. An integer parameter between 10 and 200 specifies the desired magnification as a percentage of the default scale. SSSSEEEETTTT PPPPAAAARRRRAAAAMMMMEEEETTTTEEEERRRRSSSS RasMol has a number of internal parameters that may be modi- fied using the sssseeeetttt command. These parameters control a number of program options such as rendering options and mouse button mappings. SSSSeeeetttt AAAAmmmmbbbbiiiieeeennnntttt The RasMol aaaammmmbbbbiiiieeeennnntttt parameter is used to control the amount of ambient (or surrounding) light in the scene. The aaaammmmbbbbiiiieeeennnntttt value must be between 0 and 100 that con- trols the percentage intensity of the darkest shade of an object. For a solid object, this is the intensity of surfaces facing away from the light source or in sha- dow. For depth-cued objects this is the intensity of objects furthest from the viewer. This parameter is commonly used to correct for monitors with different "gamma values" (brightness), to change how light or dark a hardcopy image appears when printed or to alter the feeling of depth for wireframe or rib- bon representations. SSSSeeeetttt AAAAxxxxeeeessss The RasMol aaaaxxxxeeeessss parameter controls the display of orthogonal co-ordinate axes on the current display. The co-ordinate axes are those used in the molecule data Sun Microsystems Last change: October 1994 12 RASMOL(1) User Commands RASMOL(1) file, and the origin is the centre of the molecule's bounding box. The sssseeeetttt aaaaxxxxeeeessss command is similar the the commands sssseeeetttt bbbboooouuuunnnnddddbbbbooooxxxx and sssseeeetttt uuuunnnniiiittttcccceeeellllllll that display the bounding box and the crystallographic unit cell respec- tively. SSSSeeeetttt BBBBaaaacccckkkkggggrrrroooouuuunnnndddd The RasMol bbbbaaaacccckkkkggggrrrroooouuuunnnndddd parameter is used to set the colour of the "canvas" background. The colour may be given as either a colour name or a comma separated tri- ple of Red, Green, Blue (RGB) components enclosed in square brackets. Typing the command hhhheeeellllpppp ccccoooolllloooouuuurrrrssss will give a list of the predefined colour names recognised by RasMol. When running under X Windows, RasMol also recognises colours in the X server's colour name data- base. The command sssseeeetttt bbbbaaaacccckkkkggggrrrroooouuuunnnndddd is synonymous with the RasMol command bbbbaaaacccckkkkggggrrrroooouuuunnnndddd.... SSSSeeeetttt BBBBoooonnnnddddMMMMooooddddeeee The RasMol sssseeeetttt bbbboooonnnnddddmmmmooooddddeeee command controls the mechanism used to select individual bonds. When using the sssseeeelllleeeecccctttt and rrrreeeessssttttrrrriiiicccctttt commands, a given bond will be selected if i) the bondmode is oooorrrr and either of the connected atoms is selected, or ii) the bondmode is aaaannnndddd and both atoms connected by the bond are selected. Hence an individual bond may be uniquely identified by using the command sssseeeetttt bbbboooonnnnddddmmmmooooddddeeee aaaannnndddd and then uniquely selecting the atoms at both ends. SSSSeeeetttt BBBBoooouuuunnnnddddBBBBooooxxxx The RasMol bbbboooouuuunnnnddddbbbbooooxxxx parameter controls the display of the current molecules bounding box on the display. The bounding box is orthogonal to the data file's original co-ordinate axes. The sssseeeetttt bbbboooouuuunnnnddddbbbbooooxxxx command is similar the the commands sssseeeetttt aaaaxxxxeeeessss and sssseeeetttt uuuunnnniiiittttcccceeeellllllll that display orthogonal co-ordinate axes and the bounding box respectively. SSSSeeeetttt DDDDiiiissssppppllllaaaayyyy This command controls the display mode within RasMol. By default, sssseeeetttt ddddiiiissssppppllllaaaayyyy nnnnoooorrrrmmmmaaaallll,,,, RasMol displays the molecule in the representation specified by the user. The command sssseeeetttt ddddiiiissssppppllllaaaayyyy sssseeeelllleeeecccctttteeeedddd changes the display mode such that the molecule is temporarily drawn so as to indicate currently selected portion of the molecule. The user specified colour scheme and representation Sun Microsystems Last change: October 1994 13 RASMOL(1) User Commands RASMOL(1) remains unchanged. In this representation all selected atoms are shown in yellow and all non selected atoms are shown in blue. The colour of the background is also changed to a dark grey to indicate the change of display mode. This command is typically only used by external Graphical User Interfaces (GUIs). SSSSeeeetttt HHHHBBBBoooonnnnddddssss The RasMol hhhhbbbboooonnnnddddssss parameter determines whether hydrogen bonds are drawn between the donor and acceptor atoms of the hydrogen bond, sssseeeetttt hhhhbbbboooonnnnddddssss ssssiiiiddddeeeecccchhhhaaaaiiiinnnn or between the alpha carbon atoms of the protein backbone and between the phosphorous atoms of the nucleic acid backbone, sssseeeetttt hhhhbbbboooonnnnddddssss bbbbaaaacccckkkkbbbboooonnnneeee.... The actual display of hydrogen bonds is controlled by the hhhhbbbboooonnnnddddssss command. Drawing hydrogen bonds between protein alpha carbons or nucleic acid phosphorous atoms is useful when the rest of the molecule is shown in only a schematic representation such as bbbbaaaacccckkkkbbbboooonnnneeee,,,, rrrriiiibbbbbbbboooonnnnssss or ssssttttrrrraaaannnnddddssss.... his parameter is similar to the RasMol ssssssssbbbboooonnnnddddssss parameter. SSSSeeeetttt FFFFoooonnnnttttSSSSiiiizzzzeeee The RasMol sssseeeetttt ffffoooonnnnttttssssiiiizzzzeeee command is used to control the size of the characters that form atom labels. This value corresponds to the height of the displayed char- acter in pixels. The maximum value of ffffoooonnnnttttssssiiiizzzzeeee is 32 pixels, and the default value is 8 pixels high. To display atom labels on the screen use the RasMol llllaaaabbbbeeeellll command and to change the colour of displayed labels, use the ccccoooolllloooouuuurrrr llllaaaabbbbeeeellllssss command. SSSSeeeetttt HHHHeeeetttteeeerrrroooo The RasMol hhhheeeetttteeeerrrroooo parameter is used to modify the `default' behaviour of the RasMol sssseeeelllleeeecccctttt command, i.e. the behaviour of sssseeeelllleeeecccctttt without any parameters. When this value is ffffaaaallllsssseeee,,,, the default sssseeeelllleeeecccctttt region does not include an heterogenous atoms (refer to the predefined set hhhheeeetttteeeerrrroooo ). When this value is ttttrrrruuuueeee,,,, the default sssseeeelllleeeecccctttt region may contain hetero atoms. This parameter is similar to the RasMol hhhhyyyyddddrrrrooooggggeeeennnn parameter which determines whether hydrogen atoms should be included in the default set. If both hhhheeeetttteeeerrrroooo and hhhhyyyyddddrrrrooooggggeeeennnn are ttttrrrruuuueeee,,,, sssseeeelllleeeecccctttt without any parameters is equivalent to sssseeeelllleeeecccctttt aaaallllllll.... SSSSeeeetttt HHHHoooouuuurrrrGGGGllllaaaassssssss The RasMol hhhhoooouuuurrrrggggllllaaaassssssss parameter allows the user to enable and disable the use of the `hour glass' cursor Sun Microsystems Last change: October 1994 14 RASMOL(1) User Commands RASMOL(1) used by RasMol to indicate that the program is currently busy drawing the next frame. The command sssseeeetttt hhhhoooouuuurrrrggggllllaaaassssssss oooonnnn enable the indicator, whilst sssseeeetttt hhhhoooouuuurrrrggggllllaaaassssssss ooooffffffff prevents RasMol from changing the cursor. This is useful when spinning the molecule, running a sequence of commands from a script file or using interprocess communication to execute complex sequences of commands. In these cases a `flashing' cursor may be distracting. SSSSeeeetttt HHHHyyyyddddrrrrooooggggeeeennnn The RasMol hhhhyyyyddddrrrrooooggggeeeennnn parameter is used to modify the `default' behaviour of the RasMol sssseeeelllleeeecccctttt command, i.e. the behaviour of sssseeeelllleeeecccctttt without any parameters. When this value is ffffaaaallllsssseeee,,,, the default sssseeeelllleeeecccctttt region does not include any hydrogen or deuterium atoms (refer to the predefined set hhhhyyyyddddrrrrooooggggeeeennnn ). When this value is ttttrrrruuuueeee,,,, the default sssseeeelllleeeecccctttt region may contain hydrogen atoms. This parameter is similar to the RasMol hhhheeeetttteeeerrrroooo parameter which determines whether heterogenous atoms should be included in the default set. If both hhhhyyyyddddrrrrooooggggeeeennnn and hhhheeeetttteeeerrrroooo are ttttrrrruuuueeee,,,, sssseeeelllleeeecccctttt without any parameters is equivalent to sssseeeelllleeeecccctttt aaaallllllll.... SSSSeeeetttt KKKKiiiinnnneeeemmmmaaaaggggeeee The RasMol sssseeeetttt kkkkiiiinnnneeeemmmmaaaaggggeeee command controls the amount of detail stored in a Kinemage output file generated by the RasMol wwwwrrrriiiitttteeee kkkkiiiinnnneeeemmmmaaaaggggeeee command. The output kinemage files are intended to be displayed by David Richardson's Mage program. sssseeeetttt kkkkiiiinnnneeeemmmmaaaaggggeeee ffffaaaallllsssseeee,,,, the default, only stores the currently displayed represen- tation in the generated output file. The command sssseeeetttt kkkkiiiinnnneeeemmmmaaaaggggeeee ttttrrrruuuueeee,,,, generates a more complex Kinemage that contains both the wireframe and backbone representa- tions as well as the co-ordinate axes, bounding box and crystal unit cell. SSSSeeeetttt MMMMeeeennnnuuuussss The RasMol sssseeeetttt mmmmeeeennnnuuuussss command enables the canvas window's menu buttons or menu bar. This command is typ- ically only used by graphical user interfaces or to create as large as image as possible when using Micro- soft Windows. SSSSeeeetttt MMMMoooouuuusssseeee The RasMol sssseeeetttt mmmmoooouuuusssseeee command sets the rotation, trans- lation, scaling and zooming mouse bindings. The default value is rrrraaaassssmmmmoooollll which is suitable for two button mice (for three button mice the second and third buttons are Sun Microsystems Last change: October 1994 15 RASMOL(1) User Commands RASMOL(1) synonymous); X-Y rotation is controlled by the first button, and X-Y translation by the second. Additional functions are controlled by holding a modifier key on the keyboard. [Shift] and the first button performs scaling, [shift] and the second button performs Z- rotation, and [control] and the first mouse button con- trols the clipping plane. The iiiinnnnssssiiiigggghhhhtttt and qqqquuuuaaaannnnttttaaaa pro- vide the same mouse bindings as other packages for experienced users. SSSSeeeetttt RRRRaaaaddddiiiiuuuussss The RasMol sssseeeetttt rrrraaaaddddiiiiuuuussss command is used to alter the behaviour of the RasMol ddddoooottttssss command depending upon the value of the ssssoooollllvvvveeeennnntttt parameter. When ssssoooollllvvvveeeennnntttt is ttttrrrruuuueeee,,,, the rrrraaaaddddiiiiuuuussss parameter controls whether a true Van der Waal's surface is generated by the ddddoooottttssss command. If the value of rrrraaaaddddiiiiuuuussss is anything other than zero, that value is used as the radius of each atom instead of it true VdW value. When the value of ssssoooollllvvvveeeennnntttt is ttttrrrruuuueeee,,,, this parameter determines the `probe sphere' (solvent) radius. The parameter may be given as an integer in rasmol units or containing a decimal point in Angstroms. The default value of this parameter is determined by the value of ssssoooollllvvvveeeennnntttt and changing ssssoooollllvvvveeeennnntttt resets rrrraaaaddddiiiiuuuussss to its new default value. SSSSeeeetttt SSSShhhhaaaaddddoooowwww The RasMol sssseeeetttt sssshhhhaaaaddddoooowwww command enables and disables ray- tracing of the currently rendered image. Currently only the spacefilling representation is shadowed or can cast shadows. Enabling shadowing will automatically disable the Z-clipping (slabbing) plane using the com- mand ssssllllaaaabbbb ooooffffffff.... Raytracing typically takes about 10s for a moderately sized protein. It is recommended that shadowing is normally disabled whilst the molecule is being transformed or manipulated, and only enabled once an appropiate viewpoint is selected, to provide a greater impression of depth. SSSSeeeetttt SSSSllllaaaabbbbMMMMooooddddeeee The RasMol ssssllllaaaabbbbmmmmooooddddeeee parameter controls the rendering method of objects cut by the slabbing (z-clipping) plane. Valid slabmode parameters are "reject", "half", "hollow", "solid" and "section". SSSSeeeetttt SSSSoooollllvvvveeeennnntttt The RasMol sssseeeetttt ssssoooollllvvvveeeennnntttt command is used to control the behaviour of the RasMol ddddoooottttssss command. Depending upon Sun Microsystems Last change: October 1994 16 RASMOL(1) User Commands RASMOL(1) the value of the ssssoooollllvvvveeeennnntttt parameter, the ddddoooottttssss command either generates a Van der Waal's or a solvent acessi- ble surface around the currently selected set of atoms. Changing this parameter automatically resets the value of the RasMol rrrraaaaddddiiiiuuuussss parameter. The command sssseeeetttt ssssoooollll---- vvvveeeennnntttt ffffaaaallllsssseeee,,,, the default value, indicates that a Van der Waal's surface should be generated and resets the value of rrrraaaaddddiiiiuuuussss to zero. The command sssseeeetttt ssssoooollllvvvveeeennnntttt ttttrrrruuuueeee indi- cates that a `Connolly' or `Richards' solvent accessi- ble surface should be drawn and sets the rrrraaaaddddiiiiuuuussss parame- ter, the solvent radius, to 1.2 Angstroms (or 300 RasMol units). SSSSeeeetttt SSSSppppeeeeccccuuuullllaaaarrrr The RasMol sssseeeetttt ssssppppeeeeccccuuuullllaaaarrrr command enables and disables the display of specular highlights on solid objects drawn by RasMol. Specular highlights appear as white reflections of the light source on the surface of the object. The current RasMol implementation uses an approximation function to generate this highlight. The specular highlights on the surfaces of solid objects may be altered by using the specular reflection coefficient, which is altered using the RasMol sssseeeetttt ssssppppeeeeccccppppoooowwwweeeerrrr command. SSSSeeeetttt SSSSppppeeeeccccPPPPoooowwwweeeerrrr The ssssppppeeeeccccppppoooowwwweeeerrrr parameter determines the shininess of solid objects rendered by RasMol. This value between 0 and 100 adjusts the reflection coeffient used in specu- lar highlight calculations. The specular highlights are enabled and disabled by the RasMol sssseeeetttt ssssppppeeeeccccuuuullllaaaarrrr com- mand. Values around 20 or 30 produce plastic looking surfaces. High values represent more shiny surfaces such as metals, while lower values produce more diffuse/dull surfaces. SSSSeeeetttt SSSSSSSSBBBBoooonnnnddddssss The RasMol ssssssssbbbboooonnnnddddssss parameter determines whether disul- phide bridges are drawn between the sulphur atoms in the sidechain (the default) or between the alpha carbon atoms in the backbone of the cysteines residues. The actual display of disulphide bridges is controlled by the ssssssssbbbboooonnnnddddssss command. Drawing disulphide bridges between alpha carbons is useful when the rest of the protein is shown in only a schematic representation such as bbbbaaaacccckkkk---- bbbboooonnnneeee,,,, rrrriiiibbbbbbbboooonnnnssss or ssssttttrrrraaaannnnddddssss.... his parameter is similar to the RasMol hhhhbbbboooonnnnddddssss parameter. Sun Microsystems Last change: October 1994 17 RASMOL(1) User Commands RASMOL(1) SSSSeeeetttt SSSSttttrrrraaaannnnddddssss The RasMol ssssttttrrrraaaannnnddddssss parameter controls the number of parallel strands that are displayed in the ribbon representations of proteins. The permissible values for this parameter are 1, 2, 3, 4, 5 and 9. The default value is 5. The number of strands is constant for all ribbons being displayed. However, the ribbon width (the separation between strands) may be controlled on a residue by residue basis using the RasMol rrrriiiibbbbbbbboooonnnnssss com- mand. SSSSeeeetttt UUUUnnnniiiittttCCCCeeeellllllll The RasMol uuuunnnniiiittttcccceeeellllllll parameter controls the display of the crystallographic unit cell on the current display. The crystal cell is only enabled if the appropriate crystal symmetry information is contained in the PDB data file. The RasMol command sssshhhhoooowwww ssssyyyymmmmmmmmeeeettttrrrryyyy display details of the crystal's space group and unit cell axes. The sssseeeetttt uuuunnnniiiittttcccceeeellllllll command is similar the the com- mands sssseeeetttt aaaaxxxxeeeessss and sssseeeetttt bbbboooouuuunnnnddddbbbbooooxxxx that display orthogonal co-ordinate axes and the bounding box respectively. SSSSeeeetttt VVVVeeeeccccttttPPPPSSSS The RasMol vvvveeeeccccttttppppssss parameter is use to control the way in which the RasMol wwwwrrrriiiitttteeee command generates vector PostScript output files. The command sssseeeetttt vvvveeeeccccttttppppssss oooonnnn enables to use of black outlines around spheres and cylinder bonds producing `cartoon-like' high resolution output. However, the current implementation of RasMol incorrectly cartoons spheres that are intersected by more than one other sphere. Hence `ball and stick' models are rendered correctly by not large spacefilling spheres models. Cartoon outlines can be disabled, the default, by the command sssseeeetttt vvvveeeeccccttttppppssss ooooffffffff AAAATTTTOOOOMMMM EEEEXXXXPPPPRRRREEEESSSSSSSSIIIIOOOONNNNSSSS RasMol atom expressions uniquely identify an arbitrary group of atoms within a molecule. Atom expressions are composed of either primitive expressions, predefined sets, comparison operators, wwwwiiiitttthhhhiiiinnnn expressions, or logical (boolean) combina- tions of the above expression types. The logical operators allow complex queries to be con- structed out of simpler ones using the standard boolean con- nectives aaaannnndddd,,,, oooorrrr and nnnnooootttt.... These may be abbreviated by the symbols "&", "|" and "!" respectively. Parentheses (brack- ets) may be used to alter the precedence of the operators. For convenience, a comma may also be used for boolean dis- junction. Sun Microsystems Last change: October 1994 18 RASMOL(1) User Commands RASMOL(1) The atom expression is evaluated for each atom, hence pppprrrroooo---- tttteeeeiiiinnnn aaaannnndddd bbbbaaaacccckkkkbbbboooonnnneeee selects protein bacbone atoms, not the protein and [nucleic] acid backbone atoms! PPPPrrrriiiimmmmiiiittttiiiivvvveeee EEEExxxxpppprrrreeeessssssssiiiioooonnnnssss RasMol primitive expressions are the fundamental build- ing blocks of atom expressions. There are two types of primitive expression. The first type is used to iden- tify a given residue number or range of residue numbers. A single residue is identified by its number (position in the sequence), and a range is specified by lower and upper bounds separated by a hyphen character. For example sssseeeelllleeeecccctttt 5555,,,,6666,,,,7777,,,,8888 is also sssseeeelllleeeecccctttt 5555----8888.... Note that this selects the given residue numbers in all macromolecule chains. The second type of primitive expression specifies a sequence of fields that must match for a given atom. The first part specifies a residue (or group of resi- dues) and an optional second part specifies the atoms within those residues. The first part consists of a residue name, optionally followed by a residue number and/or chain identifier. The second part consists of a period character followed by an atom name. An asterisk may be used as a wild card for a whole field and a question mark as a single character wildcard. CCCCoooommmmppppaaaarrrriiiissssoooonnnn OOOOppppeeeerrrraaaattttoooorrrrssss Parts of a molecule may also be distinguished using equality, inequality and ordering operators on their properties. The format of such comparison expression is a property name, followed by a comparison operator and then an integer value. The atom properties that may be used in RasMol are aaaattttoooommmmnnnnoooo for the atom serial number, eeeelllleeeemmmmnnnnoooo for the atom's atomic number (element), rrrreeeessssnnnnoooo for the residue number, rrrraaaaddddiiiiuuuussss for the spacefill radius in RasMol units (or zero if not represented as a sphere) and tttteeeemmmmppppeeeerrrraaaa---- ttttuuuurrrreeee for the PDB anisotropic temperature value. The equality operator is denoted either "=" or "==". The inequality operator as either "<>", "!=" or "/=". The ordering operators are "<" for less than, "<=" for less than or equal to, ">" for greater than, and ">" for greater than or equal to. WWWWiiiitttthhhhiiiinnnn EEEExxxxpppprrrreeeessssssssiiiioooonnnnssss A RasMol wwwwiiiitttthhhhiiiinnnn expression allows atoms to be selected Sun Microsystems Last change: October 1994 19 RASMOL(1) User Commands RASMOL(1) on their proximity to another set of atoms. A wwwwiiiitttthhhhiiiinnnn expression takes two parameters separated by a comma and surrounded by parenthesis. The first argument is an integer value called the "cut-off" distance of the within expression and the second argument is any valid atom expression. The cut-off distance is expressed in either integer RasMol units or Angstroms containing a decimal point. An atom is selected if it is within the cut-off distance of any of the atoms defined by the second argument. This allows complex expressions to be constructed containing nested wwwwiiiitttthhhhiiiinnnn expressions. For example, the command sssseeeelllleeeecccctttt wwwwiiiitttthhhhiiiinnnn((((3333....2222,,,,bbbbaaaacccckkkkbbbboooonnnneeee)))) selects any atom within a 3.2 Angstrom radius of any atom in a protein or nucleic acid backbone. WWWWiiiitttthhhhiiiinnnn expressions are particularly useful for selecting the atoms around an active site. PPPPrrrreeeeddddeeeeffffiiiinnnneeeedddd SSSSeeeettttssss RasMol atom expressions may contain predefined sets. These sets are single keywords that represent portions of a molecule of interest. Predefined sets are often abbreviations primitive atom expressions, and in some cases of selecting areas of a molecule that could not otherwise be distinguished. A list of the currently predefined sets is given below. In addition to the sets listed here, RasMol also treats element names (and their plurals) as predefined sets containing all atoms of that element type, i.e. the command sssseeeelllleeeecccctttt ooooxxxxyyyyggggeeeennnn is equivalent to the command sssseeeelllleeeecccctttt eeeelllleeeemmmmnnnnoooo====8888.... PPPPrrrreeeeddddeeeeffffiiiinnnneeeedddd SSSSeeeettttssss AAAATTTT SSSSeeeetttt This set contains the atoms in the complementary nucleotides adenosine and thymidine (A and T respec- tively). All nucleotides are classified as either the set aaaatttt or the set ccccgggg This set is equivalent to the RasMol atom expressions aaaa,,,,tttt and nnnnuuuucccclllleeeeiiiicccc aaaannnndddd nnnnooootttt ccccgggg AAAAcccciiiiddddiiiicccc SSSSeeeetttt The set of acidic amino acids. These are the residue types Asp and Glu. All amino acids are classified as either aaaacccciiiiddddiiiicccc,,,, bbbbaaaassssiiiicccc oooorrrr nnnneeeeuuuuttttrrrraaaallll.... This set is equivalent to the RasMol atom expressions aaaasssspppp,,,, gggglllluuuu and aaaammmmiiiinnnnoooo aaaannnndddd nnnnooootttt ((((bbbbaaaassssiiiicccc oooorrrr nnnneeeeuuuuttttrrrraaaallll)))) AAAAccccyyyycccclllliiiicccc SSSSeeeetttt The set of atoms in amino acids not containing a cycle Sun Microsystems Last change: October 1994 20 RASMOL(1) User Commands RASMOL(1) or ring. All amino acids are classified as either ccccyyyycccclllliiiicccc or aaaaccccyyyycccclllliiiicccc.... This set is equivalent to the RasMol atom expression aaaammmmiiiinnnnoooo aaaannnndddd nnnnooootttt ccccyyyycccclllliiiicccc AAAAlllliiiipppphhhhaaaattttiiiicccc SSSSeeeetttt This set contains the aliphatic amino acids. These are the amino acids Ala, Gly, Ile, Leu and Val. This set is equiavlent to the RasMol atom expression aaaallllaaaa,,,, ggggllllyyyy,,,, iiiilllleeee,,,, lllleeeeuuuu,,,, vvvvaaaallll AAAAllllpppphhhhaaaa SSSSeeeetttt The set of alpha carbons in the protein molecule. This set is approximately equivalent to the RasMol atom expression ****....CCCCAAAA This command should not be confused with the predefined set hhhheeeelllliiiixxxx which contains the atoms in the amino acids of the protein's alpha helices. AAAAmmmmiiiinnnnoooo SSSSeeeetttt This set contains all the atoms contained in amino acid residues. This is useful for distinguishing the pro- tein from the nucleic acid and heterogenous atoms in the current molecule database. AAAArrrroooommmmaaaattttiiiicccc SSSSeeeetttt The set of atoms in amino acids containing aromatic rings. These are the amino acids His, Phe, Trp and Tyr. Because they contain aromatic rings all members of this set are member of the predefined set ccccyyyycccclllliiiicccc.... This set is equivalent to the RasMol atom expressions hhhhiiiissss,,,, pppphhhheeee,,,, ttttrrrrpppp,,,, ttttyyyyrrrr and ccccyyyycccclllliiiicccc aaaannnndddd nnnnooootttt pppprrrroooo BBBBaaaacccckkkkbbbboooonnnneeee SSSSeeeetttt This set contains the four atoms of each amino acid that form the polypeptide N-C-C-O backbone of proteins, and the atoms the sugar phosphate backbone of nucleic acids. Use the RasMol predefined sets pppprrrrooootttteeeeiiiinnnn and nnnnuuuucccclllleeeeiiiicccc to distinguish between the two forms of back- bone. Atoms in nucleic acids and proteins are either bbbbaaaacccckkkkbbbboooonnnneeee or ssssiiiiddddeeeecccchhhhaaaaiiiinnnn.... This set is equivalent to the RasMol expression ((((pppprrrrooootttteeeeiiiinnnn oooorrrr nnnnuuuucccclllleeeeiiiicccc)))) aaaannnndddd nnnnooootttt ssssiiiiddddeeeecccchhhhaaaaiiiinnnn The predefined set mmmmaaaaiiiinnnncccchhhhaaaaiiiinnnn is synonymous with the set bbbbaaaacccckkkkbbbboooonnnneeee.... BBBBaaaassssiiiicccc SSSSeeeetttt Sun Microsystems Last change: October 1994 21 RASMOL(1) User Commands RASMOL(1) The set of basic amino acids. These are the residue types Arg, His and Lys. All amino acids are classified as either aaaacccciiiiddddiiiicccc,,,, bbbbaaaassssiiiicccc or nnnneeeeuuuuttttrrrraaaallll.... This set is equivalent to the RasMol atom expressions aaaarrrrgggg,,,, hhhhiiiissss,,,, llllyyyyssss and aaaammmmiiiinnnnoooo aaaannnndddd nnnnooootttt ((((aaaacccciiiiddddiiiicccc oooorrrr nnnneeeeuuuuttttrrrraaaallll)))) BBBBoooonnnnddddeeeedddd SSSSeeeetttt This set contain all the atoms in the current molecule database that are bonded to atleast one other atom. BBBBuuuurrrriiiieeeedddd SSSSeeeetttt This set contains the atoms in those amino acids that tend (prefer) to buried inside protein, away from con- tact with solvent molecules. This set refers to the amino acids preference and not the actual solvent aces- sibility for the current protein. All amino acids are classified as either ssssuuuurrrrffffaaaacccceeee or bbbbuuuurrrriiiieeeedddd.... This set is equivalent to the RasMol atom expression aaaammmmiiiinnnnoooo aaaannnndddd nnnnooootttt ssssuuuurrrrffffaaaacccceeee CCCCGGGG SSSSeeeetttt This set contains the atoms in the complementary nucleotides cytidine and guanoine (C and G respec- tively). All nucleotides are classified as either the set aaaatttt or the set ccccgggg This set is equivalent to the RasMol atom expressions cccc,,,,gggg and nnnnuuuucccclllleeeeiiiicccc aaaannnndddd nnnnooootttt aaaatttt CCCChhhhaaaarrrrggggeeeedddd SSSSeeeetttt This set contains the charged amino acids. These are the amino acids that are either aaaacccciiiiddddiiiicccc or bbbbaaaassssiiiicccc.... Amino acids are classified as being either cccchhhhaaaarrrrggggeeeedddd or nnnneeeeuuuu---- ttttrrrraaaallll.... This set is equivalent to the RasMol atom expres- sions aaaacccciiiiddddiiiicccc oooorrrr bbbbaaaassssiiiicccc and aaaammmmiiiinnnnoooo aaaannnndddd nnnnooootttt nnnneeeeuuuuttttrrrraaaallll CCCCyyyycccclllliiiicccc SSSSeeeetttt The set of atoms in amino acids containing a cycle or rings. All amino acids are classified as either ccccyyyycccclllliiiicccc or aaaaccccyyyycccclllliiiicccc.... This set consists of the amino acids His, Phe, Pro, Trp and Tyr. The members of the predefined set aaaarrrroooommmmaaaattttiiiicccc are members of this set. The only cyclic but non-aromatic amino acid is proline. This set is equivalent to the RasMol atom expressions hhhhiiiissss,,,, pppphhhheeee,,,, pppprrrroooo,,,, ttttrrrrpppp,,,, ttttyyyyrrrr and aaaarrrroooommmmaaaattttiiiicccc oooorrrr pppprrrroooo and aaaammmmiiiinnnnoooo aaaannnndddd nnnnooootttt aaaaccccyyyycccclllliiiicccc CCCCyyyyssssttttiiiinnnneeee SSSSeeeetttt Sun Microsystems Last change: October 1994 22 RASMOL(1) User Commands RASMOL(1) This set contains the atoms of cysteine residues that form part of a disulphide bridge, i.e. half cystines. RasMol automatically determines disulphide bridges, if neither the predefined set ccccyyyyssssttttiiiinnnneeee nor the RasMol ssssssssbbbboooonnnnddddssss command have been used since the molecule was loaded. The set of free cysteines may be determined using the RasMol atom expression ccccyyyyssss aaaannnndddd nnnnooootttt ccccyyyyssssttttiiiinnnneeee HHHHeeeelllliiiixxxx SSSSeeeetttt This set contains all atoms that form part of a protein alpha helix as determined by either the PDB file author or Kabsch and Sander's DSSP algorithm. By default, RasMol uses the secondary structure determination given in the PDB file if it exists. Otherwise, it uses the DSSP algorithm as used by the RasMol ssssttttrrrruuuuccccttttuuuurrrreeee command. This predefined set should not be confused with the predefined set aaaallllpppphhhhaaaa which contains the alpha carbon atoms of a protein. HHHHeeeetttteeeerrrroooo SSSSeeeetttt This set contains all the heterogenous atoms in the molecule. These are the atoms described by HETATM entries in the PDB file. These typically contain water, cofactors and other solvents and ligands. All hhhheeeetttteeeerrrroooo atoms are classified as either lllliiiiggggaaaannnndddd or ssssoooollllvvvveeeennnntttt atoms. These heterogenous ssssoooollllvvvveeeennnntttt atoms are further classified as either wwwwaaaatttteeeerrrr or iiiioooonnnnssss.... HHHHyyyyddddrrrrooooggggeeeennnn SSSSeeeetttt This predefined set contains all the hydrogen and deu- terium atoms of the current molecule. This predefined set is equivalent to the RasMol atom expression eeeelllleeeemmmmnnnnoooo====1111 HHHHyyyyddddrrrroooopppphhhhoooobbbbiiiicccc SSSSeeeetttt This set contains all the hydrophobic amino acids. These are the amino acids Ala, Leu, Val, Ile, Pro, Phe, Met and Trp. All amino acids are classified as either hhhhyyyyddddrrrroooopppphhhhoooobbbbiiiicccc or ppppoooollllaaaarrrr.... This set is equivalent to the RasMol atom expressions aaaallllaaaa,,,, lllleeeeuuuu,,,, vvvvaaaallll,,,, iiiilllleeee,,,, pppprrrroooo,,,, pppphhhheeee,,,, and aaaammmmiiiinnnnoooo aaaannnndddd nnnnooootttt ppppoooollllaaaarrrr IIIIoooonnnnssss SSSSeeeetttt This set contains all the heterogenous phosphate and sulphate ions in the current molecule data file. A large number of these ions are sometimes associated Sun Microsystems Last change: October 1994 23 RASMOL(1) User Commands RASMOL(1) with protein and nucleic acid structures determined by X-ray crystallography. These atoms tend to clutter an image. All hhhheeeetttteeeerrrroooo atoms are classified as either lllliiiiggggaaaannnndddd or ssssoooollllvvvveeeennnntttt atoms. All ssssoooollllvvvveeeennnntttt atoms are classified as either wwwwaaaatttteeeerrrr or iiiioooonnnnssss.... LLLLaaaarrrrggggeeee SSSSeeeetttt All amino acids are classified as either ssssmmmmaaaallllllll,,,, mmmmeeeeddddiiiiuuuummmm or llllaaaarrrrggggeeee.... This set is equivalent to the RasMol atom expression aaaammmmiiiinnnnoooo aaaannnndddd nnnnooootttt ((((ssssmmmmaaaallllllll oooorrrr mmmmeeeeddddiiiiuuuummmm)))) LLLLiiiiggggaaaannnndddd SSSSeeeetttt This set contains all the heterogenous cofactor and ligand moieties that are contained in the current molecule data file. At this set is defined to be all hhhheeeetttteeeerrrroooo atoms that are not ssssoooollllvvvveeeennnntttt atoms. Hence this set is equivalent to the RasMol atom expression hhhheeeetttteeeerrrroooo aaaannnndddd nnnnooootttt ssssoooollllvvvveeeennnntttt MMMMeeeeddddiiiiuuuummmm SSSSeeeetttt All amino acids are classified as either ssssmmmmaaaallllllll,,,, mmmmeeeeddddiiiiuuuummmm or llllaaaarrrrggggeeee.... This set is equivalent to the RasMol atom expression aaaammmmiiiinnnnoooo aaaannnndddd nnnnooootttt ((((llllaaaarrrrggggeeee oooorrrr ssssmmmmaaaallllllll)))) NNNNeeeeuuuuttttrrrraaaallll SSSSeeeetttt The set of neutral amino acids. All amino acids are classified as either aaaacccciiiiddddiiiicccc,,,, bbbbaaaassssiiiicccc or nnnneeeeuuuuttttrrrraaaallll.... This set is equivalent to the RasMol atom expression aaaammmmiiiinnnnoooo aaaannnndddd nnnnooootttt ((((aaaacccciiiiddddiiiicccc oooorrrr bbbbaaaassssiiiicccc)))) NNNNuuuucccclllleeeeiiiicccc SSSSeeeetttt The set of all atoms in nucleic acids, which consists of the four nucleotide bases adenosine, cytidine, guanosine and thymidine (A, C, G and T respectively). All neucleotides are classified as either ppppuuuurrrriiiinnnneeee or ppppyyyyrrrriiiimmmmiiiiddddiiiinnnneeee.... This set is equivalent to the RasMol atom expressions aaaa,,,,cccc,,,,gggg,,,,tttt and ppppuuuurrrriiiinnnneeee oooorrrr ppppyyyyrrrriiiimmmmiiiiddddiiiinnnneeee PPPPoooollllaaaarrrr SSSSeeeetttt This set contains the polar amino acids. All amino acids are classified as either hhhhyyyyddddrrrroooopppphhhhoooobbbbiiiicccc or ppppoooollllaaaarrrr.... This set is equivalent to the RasMol atom expression aaaammmmiiiinnnnoooo aaaannnndddd nnnnooootttt hhhhyyyyddddrrrroooopppphhhhoooobbbbiiiicccc PPPPrrrrooootttteeeeiiiinnnn SSSSeeeetttt Sun Microsystems Last change: October 1994 24 RASMOL(1) User Commands RASMOL(1) The set of all atoms in proteins. This consists of the RasMol predefined set aaaammmmiiiinnnnoooo and common post-translation modifications. PPPPuuuurrrriiiinnnneeee SSSSeeeetttt The set of purine nucleotides. These are the bases adenosine and guanosine (A and G respectively). All nucleotides are either ppppuuuurrrriiiinnnneeeessss or ppppyyyyrrrriiiimmmmiiiiddddiiiinnnneeeessss.... This set is equivalent to the RasMol atom expressions aaaa,,,,gggg and nnnnuuuucccclllleeeeiiiicccc aaaannnndddd nnnnooootttt ppppuuuurrrriiiinnnneeee PPPPyyyyrrrriiiimmmmiiiiddddiiiinnnneeee SSSSeeeetttt The set of pyrimidine nucleotides. These are the bases cytidine and thymidine (C and T respectively). All nucleotides are either ppppuuuurrrriiiinnnneeeessss or ppppyyyyrrrriiiimmmmiiiiddddiiiinnnneeeessss.... This set is equivalent to the RasMol atom expressions cccc,,,,tttt and nnnnuuuucccclllleeeeiiiicccc aaaannnndddd nnnnooootttt ppppyyyyrrrriiiimmmmiiiiddddiiiinnnneeee SSSSeeeelllleeeecccctttteeeedddd SSSSeeeetttt This set contains the set of atoms in the currently selected region. The currently selected region is defined by the preceding sssseeeelllleeeecccctttt or rrrreeeessssttttrrrriiiicccctttt command and not the atom expression containing the sssseeeelllleeeecccctttteeeedddd key- word. SSSShhhheeeeeeeetttt SSSSeeeetttt This set contains all atoms that form part of a protein beta sheet as determined by either the PDB file author or Kabsch and Sander's DSSP algorithm. By default, RasMol uses the secondary structure determination given in the PDB file if it exists. Otherwise, it uses the DSSP algorithm as used by the RasMol ssssttttrrrruuuuccccttttuuuurrrreeee command. SSSSiiiiddddeeeecccchhhhaaaaiiiinnnn SSSSeeeetttt This set contains the functional sidechains of any amino acids and the base of each nucleotide. These are the atoms not part of the polypeptide N-C-C-O backbone of proteins or the sugar phosphate backbone of nucleic acids. Use the RasMol predefined sets pppprrrrooootttteeeeiiiinnnn and nnnnuuuucccclllleeeeiiiicccc to distinguish between the two forms of sidechain. Atoms in nucleic acids and proteins are either bbbbaaaacccckkkkbbbboooonnnneeee or ssssiiiiddddeeeecccchhhhaaaaiiiinnnn.... This set is equivalent to the RasMol expression ((((pppprrrrooootttteeeeiiiinnnn oooorrrr nnnnuuuucccclllleeeeiiiicccc)))) aaaannnndddd nnnnooootttt bbbbaaaacccckkkkbbbboooonnnneeee SSSSmmmmaaaallllllll SSSSeeeetttt Sun Microsystems Last change: October 1994 25 RASMOL(1) User Commands RASMOL(1) All amino acids are classified as either ssssmmmmaaaallllllll,,,, mmmmeeeeddddiiiiuuuummmm or llllaaaarrrrggggeeee.... This set is equivalent to the RasMol atom expression aaaammmmiiiinnnnoooo aaaannnndddd nnnnooootttt ((((mmmmeeeeddddiiiiuuuummmm oooorrrr llllaaaarrrrggggeeee)))) SSSSoooollllvvvveeeennnntttt SSSSeeeetttt This set contains the solvent atoms in the molecule co-ordinate file. These are the heterogenous water molecules, phosphate and sulphate ions. All hhhheeeetttteeeerrrroooo atoms are classified as either lllliiiiggggaaaannnndddd or ssssoooollllvvvveeeennnntttt atoms. All ssssoooollllvvvveeeennnntttt atoms are classified as either wwwwaaaatttteeeerrrr or iiiioooonnnnssss.... This set is equivalent to the RasMol atom expres- sions hhhheeeetttteeeerrrroooo aaaannnndddd nnnnooootttt lllliiiiggggaaaannnndddd and wwwwaaaatttteeeerrrr oooorrrr iiiioooonnnnssss SSSSuuuurrrrffffaaaacccceeee SSSSeeeetttt This set contains the atoms in those amino acids that tend (prefer) to be on the surface of proteins, in con- tact with solvent molecules. This set refers to the amino acids preference and not the actual solvent accessibility for the current protein. All amino acids are classified as either ssssuuuurrrrffffaaaacccceeee or bbbbuuuurrrriiiieeeedddd.... This set is equivalent to the RasMol atom expression aaaammmmiiiinnnnoooo aaaannnndddd nnnnooootttt bbbbuuuurrrriiiieeeedddd TTTTuuuurrrrnnnn SSSSeeeetttt This set contains all atoms that form part of a protein turns as determined by either the PDB file author or Kabsch and Sander's DSSP algorithm. By default, RasMol uses the secondary structure determination given in the PDB file if it exists. Otherwise, it uses the DSSP algorithm as used by the RasMol ssssttttrrrruuuuccccttttuuuurrrreeee command. WWWWaaaatttteeeerrrr SSSSeeeetttt This set contains all the heterogenous water molecules in the current database. A large number of water molecules are sometimes associated with protein and nucleic acid structures determined by X-ray crystallog- raphy. These atoms tend to clutter an image. All hhhheeeetttteeeerrrroooo atoms are classified as either lllliiiiggggaaaannnndddd or ssssoooollllvvvveeeennnntttt atoms. The ssssoooollllvvvveeeennnntttt atoms are further classified as either wwwwaaaatttteeeerrrr or iiiioooonnnnssss.... CCCCOOOOLLLLOOOOUUUURRRR SSSSCCCCHHHHEEEEMMMMEEEESSSS The RasMol ccccoooolllloooouuuurrrr command allows different objects (such as atoms, bonds and ribbon segments) to be given a specified colour. Typically this colour is either a RasMol predefined colour name or an RGB triple. Additionally RasMol also sup- ports ccccppppkkkk,,,, aaaammmmiiiinnnnoooo,,,, cccchhhhaaaaiiiinnnn,,,, ggggrrrroooouuuupppp,,,, sssshhhhaaaappppeeeellllyyyy,,,, ssssttttrrrruuuuccccttttuuuurrrreeee,,,, Sun Microsystems Last change: October 1994 26 RASMOL(1) User Commands RASMOL(1) tttteeeemmmmppppeeeerrrraaaattttuuuurrrreeee,,,, cccchhhhaaaarrrrggggeeee and uuuusssseeeerrrr colour schemes for atoms, a hhhhbbbboooonnnndddd ttttyyyyppppeeee colour scheme for hydrogen bonds and eeeelllleeeeccccttttrrrroooossss---- ttttaaaattttiiiicccc ppppooootttteeeennnnttttiiiiaaaallll colour scheme for dot surfaces. The currently predefined colour names are blue, black, cyan, green, greenblue, magenta, orange, purple, red, redorange, violet, white and yellow. AAAAmmmmiiiinnnnoooo CCCCoooolllloooouuuurrrrssss The RasMol aaaammmmiiiinnnnoooo colour scheme colours amino acids according to traditional amino acid properties. The purpose of colouring is to identify amino acids in an unusual or surprising environment. The outer parts of a protein that are polar are visible (bright) colours and non-polar residues darker. Most colours are hallowed by tradition. This colour scheme is similar to the sssshhhhaaaappppeeeellllyyyy scheme. CCCChhhhaaaaiiiinnnn CCCCoooolllloooouuuurrrrssss The RasMol cccchhhhaaaaiiiinnnn colour scheme assigns each macromolec- ular chain a unique colour. This colour scheme is par- ticularly useful for distinguishing the parts of mul- timeric structure or the individual `strands' of a DNA chain. CCCCPPPPKKKK CCCCoooolllloooouuuurrrrssss The RasMol ccccppppkkkk colour scheme is based upon the colours of the popular plastic spacefilling models which were developed by Corey, Pauling and later improved by Kul- tun. This colour scheme colour `atom' objects by the atom (element) type. This is the scheme conventionally used by chemists. GGGGrrrroooouuuupppp CCCCoooolllloooouuuurrrrssss The RasMol ggggrrrroooouuuupppp colour scheme colour codes residues by their position in a macromolecular chain. Each chain is drawn as a smooth spectrum from blue through green, yellow and orange to red. Hence the N terminus of pro- teins and 5' terminus of nucleic acids are coloured red and the C terminus of proteins and 3' terminus of nucleic acids are drawn in blue. If a chain has a large number of heterogenous molecules associated with it, the macromolecule may not be drawn in the full `range' of the spectrum. SSSShhhhaaaappppeeeellllyyyy CCCCoooolllloooouuuurrrrssss The RasMol sssshhhhaaaappppeeeellllyyyy colour scheme colour codes residues by amino acid property. This scheme is based upon Bob Sun Microsystems Last change: October 1994 27 RASMOL(1) User Commands RASMOL(1) Fletterick's "Shapely Models". Each amino acid and nucleic acid residue is given a unique colour. The sssshhhhaaaappppeeeellllyyyy colour scheme is used by David Bacon's Raster3D program. This colour scheme is similar to the aaaammmmiiiinnnnoooo colour scheme. SSSSttttrrrruuuuccccttttuuuurrrreeee CCCCoooolllloooouuuurrrrssss The RasMol ssssttttrrrruuuuccccttttuuuurrrreeee colour scheme colours the molecule by protein secondary structure. Alpha helices are coloured magenta, [240,0,128], beta sheets are coloured yellow, [255,255,0], turns are coloured pale blue, [96,128,255] and all other residues are coloured white. The secondary structure is either read from the PDB file (HELIX and SHEET records), if available, or deter- mined using Kabsch and Sander's DSSP algorithm. The RasMol ssssttttrrrruuuuccccttttuuuurrrreeee command may be used to force DSSP's structure assignment to be used. TTTTeeeemmmmppppeeeerrrraaaattttuuuurrrreeee CCCCoooolllloooouuuurrrrssss The RasMol tttteeeemmmmppppeeeerrrraaaattttuuuurrrreeee colour scheme colour codes each atom according to the anisotropic temperature (beta) value stored in the PDB file. Typically this gives a measure of the mobility/uncertainty of a given atom's position. High values are coloured in warmer (red) colours and lower values in colder (blue) colours. This feature is often used to associate a "scale" value [such as amino acid variability in viral mutants] with each atom in a PDB file, and colour the molecule appropriately. The difference between the tttteeeemmmmppppeeeerrrraaaattttuuuurrrreeee and cccchhhhaaaarrrrggggeeee colour schemes is that increasing temperature values proceed from blue to red, whereas increasing charge valuse go from red to blue. CCCChhhhaaaarrrrggggeeee CCCCoooolllloooouuuurrrrssss The RasMol cccchhhhaaaarrrrggggeeee colour scheme colour codes each atom according to the charge value stored in the input file (or beta factor field of PDB files). High values are coloured in blue (positive) and lower values coloured in red (negative). Rather than use a fixed scale this scheme determines the maximum and minimum values of the charge/temperature field and interpolates from red to blue appropriately. Hence, green cannot be assumed to be `no net charge' charge. The difference between the cccchhhhaaaarrrrggggeeee and tttteeeemmmmppppeeeerrrraaaattttuuuurrrreeee colour schemes is that increasing temperature values proceed from blue to red, whereas increasing charge Sun Microsystems Last change: October 1994 28 RASMOL(1) User Commands RASMOL(1) valuse go from red to blue. If the charge/temperature field stores reasonable values it is possible to use the RasMol ccccoooolllloooouuuurrrr ddddoooottttssss ppppooootttteeeennnnttttiiiiaaaallll command to colour code a dot surface (gen- erated by the ddddoooottttssss command) by electrostatic potential. UUUUsssseeeerrrr CCCCoooolllloooouuuurrrrssss The RasMol uuuusssseeeerrrr colour scheme allows RasMol to use the colour scheme stored in the PDB file. The colours for each atom are stored in COLO records placed in the PDB data file. This convention was introduced by David Bacon's Raster3D program. HHHHBBBBoooonnnndddd TTTTyyyyppppeeee CCCCoooolllloooouuuurrrrssss The RasMol ttttyyyyppppeeee colour scheme applies only to hydrogen bonds, hence is used in the command ccccoooolllloooouuuurrrr hhhhbbbboooonnnnddddssss ttttyyyyppppeeee This scheme colour codes each hydrogen bond according to the distance along a protein chain between hydrogen bond donor and acceptor. This schematic representation was introduced by Belhadj-Mostefa and Milner-White. This representation gives a good insight into protein secondary structure (hbonds forming alpha helices appear red, those forming sheets appear yellow and those forming turns appear magenta). PPPPooootttteeeennnnttttiiiiaaaallll CCCCoooolllloooouuuurrrrssss The RasMol ppppooootttteeeennnnttttiiiiaaaallll colour scheme applies only to dot surfaces, hence is used in the command ccccoooolllloooouuuurrrr ddddoooottttssss ppppooootttteeeennnnttttiiiiaaaallll This scheme colours each currently displayed dot by the electrostatic potential at that point in space. This potential is calculated using Coulomb's law taking the temperature/charge field of the input file to be the charge assocated with that atom. This is the same interpretation used by the ccccoooolllloooouuuurrrr cccchhhhaaaarrrrggggeeee command. Like the cccchhhhaaaarrrrggggeeee colour scheme low values are blue/white and high values are red. SSSSEEEEEEEE AAAALLLLSSSSOOOO The RasMol User Manual! AAAAUUUUTTTTHHHHOOOORRRR Copyright (C) 1992-94 by Roger Sayle. All rights reserved. (rasmol@ggr.co.uk) Sun Microsystems Last change: October 1994 29