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Copyright (C) 1992,1993,1994 by Roger Sayle (rasmol@ggr.co.uk) The information supplied in this document is believed to be true but no liability is assumed for its use or for the infringements of the rights of the others resulting from its use. Information in this document is subject to change without notice and does not represent a commitment on the part of the supplier. This package is sold/distributed subject to the condition that it shall not, by way of trade or otherwise, be lent, re-sold, hired out or otherwise circulated without the supplier's prior consent, in any form of packaging or cover other than that in which it was produced. No part of this manual or accompanying software may be reproduced, stored in a retrieval system on optical or magnetic disk, tape or any other medium, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording or otherwise for any purpose other than the purchaser's personal use. This product is not to be used in the planning, construction, maintenance, operation or use of any nuclear facility nor the flight, navigation or communication of aircraft or ground support equipment. The author shall not be liable, in whole or in part, for any claims or damages arising from such use, including death, bancruptcy or outbreak of war. INTRODUCTION ============ RasMol2 is an X11 windows system tool intended for the visualisation of proteins and nucleic acids. RasMol requires either an 8bit pseudo colour or a 24bit (32bit) true colour display. The program reads in a specified Brookhaven protein databank (PDB) file and determines the connectivity from the residue information provided. This may then rendered on the screen in a variety of formats and colour schemes. Currently available molecule representations include depth-cued wireframes, sticks, space filling `union of spheres', ball and stick models and protein ribbon diagrams. COMMANDS ======== RasMol allows the execution of interactive commands typed at the "RasMol>" 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. Backbone -------- Syntax: backbone {<boolean>} backbone <value> The RasMol `backbone' command permits the representation of a polypeptide backbone as a series of bonds connecting 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 `wireframe' command. The command `backbone off' turns off the selected `bonds', and `backbone on' or with a number turns them on. The number can be used to determine the cylinder radius of the representation in 0.004 angstrom units. Backbone objects may be coloured using the RasMol `colour backbone' command. A parameter value of 500 (2 angstroms) or above results in an "Integer argument too large" error. Background ---------- Syntax: background <colour> The RasMol `background' 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 `help colours' 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 database. Centre ------ Syntax: center {<expression>} centre {<expression>} The RasMol `centre' command defines the point about which the `rotate' command and the scroll bars rotate the current molecule. Without a parameter the centre command 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 expression. Hence, if a single atom is specified by the expression, that atom will remain `stationary' during rotations. Type `help expression' for more information on RasMol atom expressions. Colour ------ Syntax: colour {<object>} <colour> color {<object>} <colour> Colour the atoms (or other objects) of the selected zone. 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 `help colours' will give a list of all the predefined colour names recognised by RasMol. Allowed objects are `atoms,' `bonds,' `backbone,' `hbonds,' `ribbons' and `ssbonds.' If no object is specified, the default keyword `atom' is assumed. Some colour schemes are defined for certain object types. The colour scheme `none' can be applied all objects accept atoms, stating that the selected objects have no colour of their own, but use the colour of their associated atoms (i.e. the atoms they connect). `Atom' objects can also be coloured by `amino,' `cpk,' `chain,' `group,' `shapely,' `structure,' `temperature' and `user' and hydrogen bond objects can also be coloured by `type.' For more information type `help colour <colour>.' HBonds ------ Syntax: hbonds {<boolean>} hbonds <value> The RasMol `hbond' 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 `hbond' 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 `hbonds on' displays the selected `bonds' as dotted lines, and the `hbonds off' turns off their display. The colour of hbond objects may be changed by the `colour hbond' 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 `set hbonds' command the alpha carbon positions of the appropriate residues may be used instead. This is especially useful when examining proteins in backbone representation. Help ---- Syntax: help {<topic> {<subtopic>}} ? {<topic> {<subtopic>} The RasMol `help' command provides on-line help on the given topic. Load ---- Syntax: load {pdb} <filename> load alchemy <filename> Load either a Brookhaven Protein Databank (PDB) file or Alchemy(tm) format file into RasMol2. Only a single PDB file may be loaded at a time. This command selects all the atoms in the molecule, and sets the default representation to be a cpk coloured wireframe model. Quit ---- Syntax: quit exit Exit from the RasMol program. Renumber -------- Syntax: renumber {{-} <value>} The RasMol `renumber' 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 proteins, 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' terminus. All chains in the current database are renumbered and gaps in the original sequence are ignored. The starting value for numbering may be negative. Reset ----- Syntax: reset The RasMol `reset' command restores the original viewing transformation and centre of rotation. The scale is set to it default value, `zoom 100,' the centre of rotation is set to the geometric centre of the currently loaded molecule, `centre all,' 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 `zap' command which deletes the currently stored molecule, returning the program to its initial state. Restrict -------- Syntax: restrict {<expression>} The RasMol `restrict' command both defines the currently active zone 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 zone. The parameter of a `restrict' command is a RasMol atom expression that is evaluated for every atom of the current molecule. This command is very similar to the RasMol `select' command, except restrict disables the `wireframe,' `spacefill' and `backbone' representations in the non-active zone. Type "help expression" for more information on RasMol atom expressions. Ribbons ------- Syntax: ribbons {<boolean>} ribbons <value> The RasMol `ribbons' command displays the currently loaded protein 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 `colour ribbon' command. If the current ribbon colour is `none' (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 this value is 380, which produces a ribbon 1.52 Angstroms wide. The number of strands in the ribbon may be altered using the RasMol `set strands' command. The rendering of the ribbon may also be changed using the `set ribbons' command. Rotate ------ Syntax: rotate <axis> {-} <value> 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. Save ---- Syntax: save {pdb} <filename> save alchemy <filename> Save the currently selected set of atoms in either a Brookhaven Protein Database (PDB) or Alchemy(tm) format file. This command should not be confused with the RasMol `write' command which generates either image or script files. Script ------ Syntax: script <filename> The RasMol `script' command reads a set of commands sequentially from a text file and executes them. This allows sequences of commonly used commands to be stored and performed by a single command. A RasMol script file may contain a further script command up to a maximum "depth" of 10, allowing compilicated sequences of actions to be executed. Select ------ Syntax: select {<expression>} Define the currently active zone of the molecule. All subsequent RasMol commands that manipulate a molecule or modify its colour or representation, only effects the currently selected zone. The parameter of a `select' command is a RasMol expression that is evaluated for every atom of the current molecule. The currently selected (active) zone of the molecule are those atoms that cause the expression to evaluate true. To select the whole molecule use the RasMol command `select all.' Type "help expression" for more information on RasMol atom expressions. Set --- Syntax: set <parameter> {<option>} The RasMol `set' 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. For more information on each internal parameter type `help set <parameter>.' Show ---- Syntax: show information show sequence The RasMol `show' command display details of the status of the currently loaded molecule. The command `show information' 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 `show sequence' lists the residues that compose each chain of the molecule. Slab ---- Syntax: slab {<boolean>} slab <value> The RasMol `slab' 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. Integer 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. Spacefill --------- Syntax: spacefill {<boolean>} spacefill temperature spacefill user spacefill <value> Represent the currently selected zone as a spacefilling union of spheres model. An integer parameter may be used to specify the radius of each atom given in 4nm units. If no parameter is given, each atom is drawn as a sphere of its Van der Waals radius. The `temperature' option is used to set the radius of each selected sphere to the value in the temperature field of the molecule file. A zero or negative value causes no change in the selected atom. Temperature values greater than 2.00 are truncated to 2.00 Angstrom radius. The `user' option allows the radius of the selected spheres to be determined by matching each atom against optional lines in the input data file. Details of the wildcard pattern matching used by Raster3D's COLOR records is given in the manual. SSBonds ------- Syntax: ssbonds {<boolean>} ssbonds <value> The RasMol `ssbonds' command is used to represent the disulphide bridges of the protein molecule as either dotted lines or cylinders between the connected cysteines. The first time that the `ssbonds' command is used, the program searches the structure of the protein 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 `ssbonds on' displays the selected `bonds' as dotted lines, and the command `ssbonds off' 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 `set bondmode' command. The colour of disulphide bonds may be changed using the `colour ssbonds' command. By default, each disulphide bond has the colours of its connected atoms. By default disulphide bonds are drawn between the sulphur atoms within the cysteine groups. By using the `set ssbonds' command the position of the cysteine's alpha carbons may be used instead. Structure --------- Syntax: structure The RasMol `structure' command calculates secondary structure assignments for the currently loaded protein. If the original PDB file contained structural assignment 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 secondary structure is the determined using Kabsch and Sander's DSSP algorithm. Once finished the program reports the number of helices and ladders found. Translate --------- Syntax: translate <axis> {-} <value> The RasMol `translate' command moves the position of the centre of the molecule on the screen. The axis parameter 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" displacement moves the molecule to the right, and a positive "y" displacement moves the molecule down the screen. The pair of commands `translate x 0' and `translate y 0' centres the molecule on the screen. Wireframe --------- Syntax: wireframe {<boolean>} wireframe <value> Represent each bond within the selected zone of the molecule as either a cylinder or depth-cued vector. If no parameter is given, RasMol draws each bond as a hither-and-yon shaded narrow vector. An integer parameter specifies the radius of a cylinder, given in 4nm units, to be used as a stick bond. Write ----- Syntax: write {<format>} <filename> Write the current image to a file in a standard raster format. Currently supported file formats include "gif" (Compuserve GIF), "ppm" (Portable Pixmap), "ras" (Sun rasterfile), "ps" and "epsf" (Encapsulated PostScript), "monops" (Monochrome Encapsulated PostScript) and "bmp" (Microsoft bitmap). This command should not be confused with the RasMol `save' command which save the currently selected portion of the molecule. Zap --- Syntax: zap Deletes the contents of the current database and resets parameter variables to their initial default state. Zoom ---- Syntax: zoom {<boolean>} zoom <value> 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. INTERNAL PARAMETERS =================== RasMol has a number of internal parameters that may be modified using the `set' command. These parameters control a number of program options such as rendering options and mouse button mappings. Set Ambient ----------- Syntax: set ambient {<value>} The RasMol `ambient' parameter is used to control the amount of ambient (or surrounding) light in the scene. The `ambient' value must be between 0 and 100 that controls 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 shadow. 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 ribbon representations. Set Background -------------- Syntax: set background <colour> The RasMol `background' 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 triple of Red, Green, Blue (RGB) components enclosed in square brackets. Typing the command `help colours' 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 database. Set BondMode ------------ Syntax: set bondmode and set bondmode or set bondmode Set Display ----------- Syntax: set display selected set display normal set display Set HBonds ---------- Syntax: set hbonds backbone set hbonds sidechain set hbonds Set Hetero ---------- Syntax: set hetero <boolean> set hetero Set HourGlass ------------- Syntax: set hourglass <boolean> The RasMol `hourglass' parameter allows the user to enable and disable the use of the `hour glass' cursor used by RasMol to indicate that the program is currently busy drawing the next frame. The command `set hourglass on' enable the indicator, whilst `set hourglass off' 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. Set Hydrogen ------------ Syntax: set hydrogen <boolean> set hydrogen Set Mouse --------- Syntax: set mouse rasmol set mouse insight set mouse quanta The RasMol `set mouse' command sets the rotation, translation, scaling and zooming mouse bindings. The default value is `rasmol' which is suitable for two button mice (for three button mice the second and third buttons are 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 controls the clipping plane. The `insight' and `quanta' provide the same mouse bindings as other packages for experienced users. Set Ribbons ----------- Syntax: set ribbons strands set ribbons solid The RasMol `set ribbons' command controls the way that macromolecular ribbons are displayed. The default value `strands' display macromolecular ribbons as parallel depth-cued strands that pass along the protein or nucleic acid backbone. The number of strands in the ribbon may be altered using the RasMol `set strands' command. The `set ribbons solid' command renders the macromolecular ribbon as a solid shaded ribbon. Set Shadow ---------- Syntax: set shadow <boolean> The RasMol `set shadow' command enables and disables raytracing 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 command `slab off.' 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. Set SlabMode ------------ Syntax: set slabmode <slabmode> The RasMol `slabmode' parameter controls the rendering method of objects cut by the slabbing (z-clipping) plane. Valid slab modes are "reject", "half", "hollow", "solid" and "section". Set Specular ------------ Syntax: set specular <boolean> The RasMol `set specular' 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 `set specpower' command. Set SpecPower ------------- Syntax: set specpower {<value>} The `specpower' parameter determines the shininess of solid objects rendered by RasMol. This value between 0 and 100 adjusts the reflection coeffient used in specular highlight calculations. The specular highlights are enabled and disabled by the RasMol `set specular' command. 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. Set SSBonds ----------- Syntax: set ssbonds backbone set ssbonds sidechain set ssbonds Set Strands ----------- Syntax: set strands {<value>} The RasMol `strands' 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 `ribbons' command. ATOM EXPRESSIONS ================ 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, `within' expressions, or logical (boolean) combinations of the above expression types. The logical operators allow complex queries to be constructed out of simpler ones using the standard boolean connectives `and, or' and `not.' These may be abbreviated by the symbols "&", "|" and "!" respectively. Parentheses (brackets) may be used to alter the precedence of the operators. For convenience, a comma may also be used for boolean disjunction. The atom expression is evaluated for each atom, hence `protein and backbone' selects protein bacbone atoms, not the protein and [nucleic] acid backbone atoms! Example Expressions ------------------- The following table gives some useful examples of RasMol atom expressions. Primitive Expressions --------------------- RasMol primitive expressions are the fundamental building blocks of atom expressions. There a two basic types of primitive expression. The first type is used to identify 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 `select 5,6,7,8' is also `select 5-8.' 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 residues) 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. A residue name typically consists of up to three alphabetic characters, which are case insensitive. Hence the primitive expressions `SER' and `ser' are equivalent, identifying all cysteine residues. Residue names that contain non-alphabetic characters, such as sulphate groups, may be delimited using square brackets, i.e. `[SO4]' The residue number is the residue's position in the macromolecule sequence. Negative sequence numbers are permited. For example, `SER70' Care must be taken when specifying both residue name and number, it the group at the specified position isn't the specified residue no atoms are selected. The chain identifier is typically a single case-insensitive alphabetic or numeric character. Numeric chain identifiers must be distinguished or separated from residue numbers by a colon character. For example, `SER70A' or `SER70:1' The second part consists of a period character followed by an atom name. An atom name may be up to four alphabetic or numeric characters. An asterisk may be used as a wild card for a whole field and a question mark as a single character wildcard. Comparison Operators -------------------- 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 `atomno' for the atom serial number, `resno' for the residue number, `radius' for the spacefill radius in RasMol units (or zero if not represented as a sphere) and `temperature' 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. Within Expressions ------------------ A RasMol `within' expression allows atoms to be selected on their proximity to another set of atoms. A `within' 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 RasMol 0.004 Angstrom units. 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 `within' expressions. For example, the command `select within(800,backbone)' selects any atom within a 3.2 Angstrom radius of any atom in a protein or nucleic acid backbone. `Within' expressions are particularly usefull for selecting the atoms around an active site. Predefined Sets --------------- RasMol atom expressions may contain predefined sets. Thsese 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 predfined sets is given below. AT Set ------ This set contains the atoms in the complementary nucleotides adenosine and thymidine (A and T respectively). All nucleotides are classified as either the set `at' or the set `cg' This set is equivalent to the RasMol atom expressions "a,t" and "nucleic and not cg" Acidic Set ---------- The set of acidic amino acids. These are the residue types Asp, Glu and Tyr. All amino acids are classified as either `acidic,' `basic' `or' `neutral.' This set is equivalent to the RasMol atom expressions "asp, glu, tyr" and "amino and not (basic or neutral)" Acyclic Set ----------- The set of atoms in amino acids not containing a cycle or ring. All amino acids are classified as either `cyclic' or `acyclic.' This set is equivalent to the RasMol atom expression "amino and not cyclic" Aliphatic Set ------------- 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 "ala, gly, ile, leu, val" Alpha Set --------- The set of alpha carbons in the protein molecule. This set is approximately equivalent to the RasMol atom expression "*.CA" This command should not be confused with the predefined set `helix' which contains the atoms in the amino acids of the protein's alpha helices. Amino Set --------- This set contains all the atoms contained in amino acid residues. This is useful for distinguishing the protein from the nucleic acid and heterogenous atoms in the current molecule database. Aromatic Set ------------ 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 `cyclic.' This set is equivalent to the RasMol atom expressions "his, phe, trp, tyr" and "cyclic and not pro" Backbone Set ------------ 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 `protein' and `nucleic' to distinguish between the two forms of backbone. Atoms in nucleic acids and proteins are either `backbone' or `sidechain.' This set is equivalent to the RasMol expression "(protein or nucleic) and not sidechain Basic Set --------- The set of basic amino acids. These are the residue types Asp, Glu and Tyr. All amino acids are classified as either `acidic,' `basic' or `neutral.' This set is equivalent to the RasMol atom expressions "asp, glu, tyr" and "amino and not (acidic or neutral)" Buried Set ---------- This set contains the atoms in those amino acids that tend (prefer) to buried inside protein, away from contact with solvent molecules. This set refers to the amino acids preference and not the actual solvent acessibility for the current protein. All amino acids are classified as either `surface' or `buried.' This set is equivalent to the RasMol atom expression "amino and not surface" CG Set ------ This set contains the atoms in the complementary nucleotides cytidine and guanoine (C and G respectively). All nucleotides are classified as either the set `at' or the set `cg' This set is equivalent to the RasMol atom expressions "c,g" and "nucleic and not at" Charged Set ----------- This set contains the charged amino acids. These are the amino acids that are either `acidic' or `basic.' Amino acids are classified as being either `charged' or `neutral.' This set is equivalent to the RasMol atom expressions "acidic or basic" and "amino and not neutral" Cyclic Set ---------- The set of atoms in amino acids containing a cycle or rings. All amino acids are classified as either `cyclic' or `acyclic.' This set consists of the amino acids His, Phe, Pro, Trp and Tyr. The members of the predefined set `aromatic' are members of this set. The only cyclic but non-aromatic amino acid is proline. This set is equivalent to the RasMol atom expressions "his, phe, pro, trp, tyr" and "aromatic or pro" and "amino and not acyclic" Cystine Set ----------- 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 `cystine' nor the RasMol `ssbonds' command have been used since the molecule was loaded. The set of free cysteines may be determined using the RasMol atom expression "cys and not cystine" Helix Set --------- 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 `structure' command. This command should not be confused with the predefined set `alpha' which contains the alpha carbon atoms of a protein. Hetero Set ---------- 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. The RasMol predefined set `water' is often used to partition this set. Hydrogen Set ------------ This predefined set contains all the hydrogen and deuterium atoms of the current molecule. Hydrophobic Set --------------- 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 `hydrophobic' or `polar.' This set is equivalent to the RasMol atom expressions "ala, leu, val, ile, pro, phe, met, trp" and "amino and not polar" Large Set --------- All amino acids are classified as either `small,' `medium' or `large.' This set is equivalent to the RasMol atom expression "amino and not (small or medium)" Medium Set ---------- All amino acids are classified as either `small,' `medium' or `large.' This set is equivalent to the RasMol atom expression "amino and not (large or small)" Neutral Set ----------- The set of neutral amino acids. All amino acids are classified as either `acidic,' `basic' `or' `neutral.' This set is equivalent to the RasMol atom expression "amino and not (acidic or basic)" Nucleic Set ----------- The set of all atoms in nucleic acids. Polar Set --------- This set contains the polar amino acids. All amino acids are classified as either `hydrophobic' or `polar.' This set is equivalent to the RasMol atom expression "amino and not hydrophobic" Protein Set ----------- The set of all atoms in proteins. This consists of the RasMol predefined set `amino' and common post-translation modifications. Purine Set ---------- The set of purine nucleotides. These are the bases adenosine and guanosine (A and G respectively). All nucleotides are either `purines' or `pyrimidines.' This set is equivalent to the RasMol atom expressions "a,g" and "nucleic and not purine" Pyrimidine Set -------------- The set of pyrimidine nucleotides. These are the bases cytidine and thymidine (C and T respectively). All nucleotides are either `purineset purines' or `pyrimidines.' This set is equivalent to the RasMol atom expressions "c,t" and "nucleic and not pyrimidine" Selected Set ------------ This set contains the set of atoms in the currently active zone. The currently active zone is defined by the preceding `select' or `restrict' command and not the atom expression containing the `selected' keyword. Sheet Set --------- 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 `structure' command. Sidechain Set ------------- 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 `protein' and `nucleic' to distinguish between the two forms of sidechain. Atoms in nucleic acids and proteins are either `backbone' or `sidechain.' This set is equivalent to the RasMol expression "(protein or nucleic) and not backbone Small Set --------- All amino acids are classified as either `small,' `medium' or `large.' This set is equivalent to the RasMol atom expression "amino and not (medium or large)" Surface Set ----------- This set contains the atoms in those amino acids that tend (prefer) to be on the surface of proteins, in contact with solvent molecules. This set refers to the amino acids preference and not the actual solvent acessibility for the current protein. All amino acids are classified as either `surface' or `buried.' This set is equivalent to the RasMol atom expression "amino and not buried" Turn Set -------- 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 `structure' command. Water Set --------- 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 crystallography. These atoms tend to clutter an image. Colour Schemes ============== The RasMol `colour' 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 supports `amino,' `chain,' `group,' `shapely,' `structure,' `temperature,' `user' and `hbond type' colour schemes. The currently predefined colour names are Amino Colours ------------- The RasMol `amino' 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 are polar are visible (bright) colours and non-polar residues darker. Most colours are hallowed by tradition. This colour scheme is similar to the `shapely' scheme. Chain Colours ------------- The RasMol `chain' colour scheme assigns each macromolecular chain a unique colour. This colour scheme is particularly usefull for distinguishing the parts of multimeric structure or the individual `strands' of a DNA chain. CPK Colours ----------- The RasMol `cpk' colour scheme is based upon the colours of the popular plastic spacefilling models which were developed by Corey, Pauling and later improved by Kultun. This colour scheme colour `atom' objects by the atom (element) type. This is the scheme conventionally used by chemists. Group Colours ------------- The RasMol `group' 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 proteins 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. Shapely Colours --------------- The RasMol `shapely' colour scheme colour codes residues by amino acid property. This scheme is based upon Bob Fletterick's "Shapely Models". Each amino acid and nucleic acid residue is given a unique colour. The `shapely' colour scheme is used by David Bacon's Raster3D program. This colour scheme is similar to the `amino' colour scheme. Structure Colours ----------------- The RasMol `structure' colour scheme colours the molecule by protein secondary structure. Alpha helices are coloured magenta, beta sheets are coloured yellow, 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 determined using Kabsch and Sander's DSSP algorithm. The RasMol `structure' command may be used to force DSSP's structure assignment to be used. Temperature Colours ------------------- The RasMol `temperature' 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. User Colours ------------ The RasMol `user' 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 introducted by David Bacon's Raster3D program. HBond Type Colours ------------------ The RasMol `type' colour scheme applies only to hydrogen bonds, hence is used in the command "colour hbonds type" This colour 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).