If the selected bonds involved atoms of alternate conformers then the bonds are narrowed in the middle to a radius of. Non-bonded atoms, which could become invisible in an ordinary ' wireframe ' display can be marked by a preceding ' set bondmode not bonded ' command. If nearly co-linear bonds to atoms cause them to be difficult to see in a wireframe display, the ' set bondmode all ' command will add markers for ' all ' atoms in subsequent ' wireframe ' command executions.
The ' write ' command may also be used to generate command scripts for other graphics programs. The format ' script ' writes out a file containing the RasMol ' script ' commands to reproduce the current image. The format ' molscript ' writes out the commands required to render the current view of the molecule as ribbons in Per Kraulis' Molscript program and the format ' kinemage ' the commands for David Richardson's program Mage. Finally, several formats are provided to provide phi-psi data for listing or for ' phipsi ' phi-psi data as an annotated list with cis omegas , ' ramachan ' and ' RDF ' and ' RamachandranDataFile ' phi-psi data as columns of numbers for gnuplot , ' RPP ' and ' RamachandranPrinterPlot ' phi-psi data as a printer plot.
The distinction between this command and the RasMol ' save ' command has been dropped. Zap Syntax: zap Deletes the contents of the current database and resets parameter variables to their initial default state. Boolean parameters either magnify or reset the scale of current molecule. An integer parameter specifies the desired magnification as a percentage of the default scale. The minimum parameter value is 10; the maximum parameter value is dependent upon the size of the molecule being displayed.
For medium sized proteins this is about 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. A complete list of internal parameter names is given below. The ' ambient ' value must be between 0 and It 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.
The coordinate axes are those used in the molecule data file, and the origin is the centre of the molecule's bounding box. The ' set axes ' command is similar to the commands ' set boundbox ' and ' set unitcell ' that display the bounding box and the crystallographic unit cell, respectively. This is controlled by the commands ' set backfade on ' and ' set backfade off '. For example, this may be used to generate depth-cued images that fade to white, rather than black.
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. The command ' set background ' is synonymous with the RasMol command ' background '.
Set BondMode Syntax: set bondmode and set bondmode or set bondmode all set bondmode none set bondmode not bonded The RasMol ' set bondmode ' command controls the mechanism used to select individual bonds and modifies the display of bonded and non-bonded atoms by subsequent ' wireframe ' commands. When using the ' select ' and ' restrict ' commands, a given bond will be selected if i the bondmode is ' or ' and either of the connected atoms is selected, or ii the bondmode is ' and ' and both atoms connected by the bond are selected.
Hence an individual bond may be uniquely identified by using the command ' set bondmode and ' and then uniquely selecting the atoms at both ends. The ' bondmode [all none not bonded] ' commands add ' star 75 ' or ' spacefill 75 ' markers for the designated atoms to ' wireframe ' displays.
Stars are used when the specified wireframe radius is zero. The command ' set bonds on ' enables the display of bond orders, and the command ' set bonds off ' disables them. The bounding box is orthogonal to the data file's original coordinate axes. The ' set boundbox ' command is similar to the commands ' set axes ' and ' set unitcell ' that display orthogonal coordinate axes and the bounding box, respectively. If no value is given, the cutoff is set to 90 degrees. Set Display Syntax: set display selected set display normal This command controls the display mode within RasMol.
By default, ' set display normal ', RasMol displays the molecule in the representation specified by the user. The command ' set display selected ' 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 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 value corresponds to the height of the displayed character in pixels. The maximum value of ' fontsize ' is 48 pixels, and the default value is 8 pixels high. Fixed or proportional spacing may be selected by appending the "FS" or "PS" modifiers, respectively.
The default is "FS". To display atom labels on the screen use the RasMol ' label ' command and to change the colour of displayed labels, use the ' colour labels ' command.
This value is the radius in pixels of cylinders used to form the strokes. The special value of "0" is the default used for the normal single pixel stroke width, which allows for rapid drawing and rotation of the image. Non-zero values are provided to allow for more artistic atom labels for publication at the expense of extra time in rendering the image.
When wider strokes are used, a larger font size is recommend, e. Set HBonds Syntax: set hbonds backbone set hbonds sidechain The RasMol ' hbonds ' parameter determines whether hydrogen bonds are drawn between the donor and acceptor atoms of the hydrogen bond, ' set hbonds sidechain ' or between the alpha carbon atoms of the protein backbone and between the phosphorous atoms of the nucleic acid backbone, ' set hbonds backbone '.
The actual display of hydrogen bonds is controlled by the ' hbonds ' 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 ' backbone ', ' ribbons ' or ' strands '. This parameter is similar to the RasMol ' ssbonds ' parameter.
When this value is ' false ', the default ' select ' region does not include any heterogeneous atoms refer to the predefined set ' hetero '. When this value is ' true ', the default ' select ' region may contain hetero atoms. This parameter is similar to the RasMol ' hydrogen ' parameter which determines whether hydrogen atoms should be included in the default set. If both ' hetero ' and ' hydrogen ' are ' true ', ' select ' without any parameters is equivalent to ' select all '.
The command ' set hourglass on ' enables 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. When this value is ' false ', the default ' select ' region does not include any hydrogen, deuterium or tritium atoms refer to the predefined set ' hydrogen '.
When this value is ' true ', the default ' select ' region may contain hydrogen atoms. This parameter is similar to the RasMol ' hetero ' parameter which determines whether heterogeneous atoms should be included in the default set.
If both ' hydrogen ' and ' hetero ' are ' true ', ' select ' without any parameters is equivalent to ' select all '. The output kinemage files are intended to be displayed by David Richardson's Mage program. The command ' set kinemage true ', generates a more complex Kinemage that contains both the wireframe and backbone representations as well as the coordinate axes, bounding box and crystal unit cell.
This command is typically only used by graphical user interfaces or to create as large an image as possible when using Microsoft Windows. The distance monitor labels may be turned off with the command ' set monitor off ', and re-enabled with the command ' set monitor on '. 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. The ' insight ' and ' quanta ' options provide the same mouse bindings as other packages for experienced users.
This behavior may be disabled with the command ' set picking none ' and restored with the command ' set picking ident '. The command ' set picking coord ' adds the atomic coordinates of the atom to the display. Disabling picking, by using ' set picking off ' is useful when executing the ' pause ' command in RasMol scripts as it prevents the display of spurious message on the command line while the script is suspended.
Measuring Distances, Angles and Torsions : Interactive measurement of distances, angles and torsions is achieved using the commands: ' set picking distance ', ' set picking monitor ', ' set picking angle ' and ' set picking torsion ', respectively. In these modes, clicking on an atom results in it being identified on the rasmol command line. In addition every atom picked increments a modulo counter such that in distance mode, every second atom displays the distance or distance monitor between this atom and the previous one.
In angle mode, every third atom displays the angle between the previous three atoms and in torsion mode every fourth atom displays the torsion between the last four atoms. By holding down the shift key while picking an atom, this modulo counter is not incremented and allows, for example, the distances of consecutive atoms from a fixed atom to be displayed. See the ' monitor ' command for how to control the display of distance monitor lines and labels. Labelling Atoms with the Mouse : The mouse may also be used to toggle the display of an atom label on a given atom.
The RasMol command ' set picking label ' removes a label from a picked atom if it already has one or displays a concise label at that atom position otherwise.
Centring Rotation with the Mouse : A molecule may be centred on a specified atom position using the RasMol commands ' set picking centre ' or ' set picking center '. In this mode, picking an atom causes all futher rotations to be about that point. Picking a Bond as a Rotation Axis : Any bond may be picked as an axis of rotation for the portion of the molecule beyond the second atom selected. This feature should be used with caution, since, naturally, it changes the conformation of the molecule.
After executing ' set picking bond ' or using the equivalent "Pick Bond" in the "Settings" menu, a bond to be rotated is picked with the same sort of mouse clicks as are used for picking atoms for a distance measurement. Normally this should be done where a bond exists, but if no bond exists, it will be added. The bond cannot be used for rotation if it is part of a ring of any size.
All bonds selected for rotation are remembered so that they can be properly reported when writing a script, but only the most recently selected bond may be actively rotated.
For each of these commands, the shift key may be used to have a new selection added to the old, and the control key may be used to have a new selection deleted from the old. When the ' set picking atom ' command is given, the mouse can be used to pick or to drag a box around the atoms for which selection is desired.
When the ' set picking group ' command is given, picking any an atom will cause selection of all atoms which agree in residue number with the picked atom, even if in different chains. When the ' set picking chain ' command is given, picking any atom will cause selection of all atoms which agree in chain identifier with the picked atom. Set Play Syntax: set play. In the current release of RasMol, the play timing is not controlled by this parameter. When ' solvent ' is ' true ', the ' radius ' parameter controls whether a true van der Waals' surface is generated by the ' dots ' command.
If the value of ' radius ' is anything other than zero, that value is used as the radius of each atom instead of its true vdW value. When the value of ' solvent ' is ' true ', this parameter determines the 'probe sphere' solvent radius. The default value of this parameter is determined by the value of ' solvent ' and changing ' solvent ' resets ' radius ' to its new default value.
Set Record Syntax: set record. The RasMol ' set record. This value between 0 and adjusts shading on an object surface oriented along the direction to the light source. Changing the shadepower parameter does not change the maximum or the minimum values of this shading, as does changing the ' ambient ' parameter. A value of concentrates the light on the top of spheres, giving a highly specular, glassy rendering see the ' specpower ' parameter. A value of 0 distributes the light on the entire object.
This implementation of shadepower differs from the one in RasTop only in the choice of range 0 to versus to 20 in RasTop. 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 '. Ray-tracing typically takes about several seconds for a moderately sized protein. It is recommended that shadowing be 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.
Valid slabmode parameters are " reject ", " half ", " hollow ", " solid " and " section ". Depending upon the value of the ' solvent ' parameter, the ' dots ' command either generates a van der Waals' or a solvent accessible surface around the currently selected set of atoms. Changing this parameter automatically resets the value of the RasMol ' radius ' parameter. The command ' set solvent false ', the default value, indicates that a van der Waals' surface should be generated and resets the value of ' radius ' to zero.
The command ' set solvent true ' indicates that a 'Connolly' or 'Richards' solvent accessible surface should be drawn and sets the ' radius ' parameter, the solvent radius, to 1. 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.
This value between 0 and adjusts the reflection coefficient 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. Set SSBonds Syntax: set ssbonds backbone set ssbonds sidechain The RasMol ' ssbonds ' parameter determines whether disulphide 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 ' ssbonds ' command. Drawing disulphide bridges between alpha carbons is useful when the rest of the protein is shown in only a schematic representation such as ' backbone ', ' ribbons ' or ' strands '.
This parameter is similar to the RasMol ' hbonds ' parameter. Turning stereo on and off doesn't reposition the centre of the molecule. Currently, stereo viewing is not supported in ' vector PostScript ' output files. 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.
This may be controlled by the ' set transparent on ' and ' set transparent off ' commands. The RasMol command ' show symmetry ' display details of the crystal's space group and unit cell axes. The ' set unitcell ' command is similar to the commands ' set axes ' and ' set boundbox ' that display orthogonal coordinate axes and the bounding box, respectively.
The command ' set vectps on ' enables the 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 but not large spacefilling spheres models. Cartoon outlines can be disabled, the default, by the command ' set vectps off '.
By default, this value is ' false ', prohibiting the generation of files in any scripts executed at start-up such as those launched from a WWW browser. However, animators may start up RasMol interactively: type ' set write on ' and then execute a script to generate each frame using the source 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 '. 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 backbone atoms, not the protein and [nucleic] acid backbone atoms!
Examples: backbone and not helix within 8. Nitrogen atoms cys. There are two 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 '. 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. 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 serine residues. Residue names that contain non-alphabetic characters, such as sulphate groups, may be delimited using square brackets, i. The residue number is intended to be the residue's position in the macromolecule sequence, but negative sequence numbers, gaps in numbering, or even reverse numbering are permitted in the PDB format.
Care must be taken when specifying both residue name and number. If the group at the specified position isn't the specified residue then 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. 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 optional semicolon followed by an alternate conformation identifier may be appended. An optional slash followed by a model number may also be appended.
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, ' elemno ' for the atom's atomic number element , ' 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 isotropic temperature value.
A ' within ' expression takes two parameters separated by a comma and surrounded by parentheses. 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. 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 3. Predefined Sets 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 of primitive atom expressions. In some cases the use of predefined sets allows selection of 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. 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 and Glu. All amino acids are classified as either ' acidic ', ' basic ' ' or ' ' neutral '. This set is equivalent to the RasMol atom expressions " asp, glu " 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 '. Department of Energy, the U. National Science Foundation and the U. Los valores permitidos para el eje son "x", "y" y "z".
La diferencia existente entre esta orden y write se ha eliminado. Los archivos script a menudo se comentan usando el comando de RasMol echo. La orden ' show centre ' muestra cualquier valor de centro diferente a cero seleccionado por comando ' centre [CenX,CenY,CenZ] '. La orden ' show rotation ' o ' show rot ' o ' show rotate ' muestra los valores actualmente seleccionados de z, de y, de x y de rotaciones en enlace, si cualquiera.
Un valor igual o superior a 2. El color de los enlaces de disulfuro se puede cambiar con la orden colour ssbonds. Por defecto. Un valor de 2. Valores de cero o negativos no tienen efecto y los valores mayores de 2.
La orden colour ribbon cambia el color de la cinta. Si el color de la cinta con la que trabajamos es el inicial none ninguno , adopta el color del carbono alfa con el que se encuentre en su recorrido longitud. Esta orden es parecida a ribbons , que representa la cinta biomolecular como una superficie sombreada lisa. Advierta que cada residuo puede ser visualizado como "ribbon", "strands", "cartoon" o trace, y activando una de esas representaciones se inactivan las otras.
Trace temperature permite visualizar la columna como un cilindro mas ancho para factores de alta temperatura y mas delgado para factores de baja. Los enlaces pueden ser coloreados con la orden ' colour bonds '.
La diferencia entre este comando y ' save ' se ha eliminado. Esta orden altera el aumento de la imagen visualizada. Se puede "sombrear" un color de fondo arbitrario, en lugar del simplemente negro.
Se controla con los comandos "set backfade on" y "set backfade off". Puede especificarse el color con el nombre correspondiente, o bien por medio de componentes tripletes de Rojo, Verde y Azul RVA separados por comas y delimitados por corchetes.
Help colours proporciona una lista de los nombres de colores predefinidos y reconocidos por RasMol. La orden de RasMol set bondmode controla el mecanismo utilizado para seleccionar enlaces individuales. Por defecto, el extremo C -terminal de las hojas beta se visualiza como cabeza de flecha. Si no se le atribuye valor, defectivamente ajusta a 90 grados. Por defecto se activa "FS". Este valor asigna el radio, en pixeles, de los cilindros usados para formar los trazos.
Cuando se desee un mayor ancho de trazo, se recomienda una mayor fuente, e. El conjunto de caracteres usado para las presentaciones por RasMol con espaciado fijo y ancho de trazo de un solo pixel y espaciado proporcional y con cilindros de trazo de 2 pixeles se muestra en la siguiente muestra:. La orden set hourglass on activa el indicador; mientras que set hourglass off impide a RasMol cambiar el cursor.
Las etiquetas de monitor a distancia distance monitor labels pueden ser anuladas con la orden set monitors off , y restablecidas con la orden set monitors on. Esta conducta se desactiva con la orden ' set picking none ' y se restaura con ' set picking ident '. Midiendo distancias, angulos y torsiones. Un valor de 0 distribuye la luz en el objeto entero. La orden de RasMol set shadow activa y desactiva el trazado de rayos de la imagen representada, lo que produce sombras.
La orden de RasMol set solvent controla el comportamiento de la orden dots. Los haces de luces especulares aparecen como reflejos blancos de la fuente de luz sobre la superficie del objeto.
La orden set specular activa y desactiva estos haces de luces especulares. El valor inicial es 5. Por lo tanto, los modelos "ball and stick" son representados correctamente pero no los modelos de esferas spacefilling. Hay dos tipos de expresiones primitivas. Por ejemplo select 5,6,7,8 es lo mismo que select Esto permite expresiones complejas usando expresiones within anidadas.
Por ejemplo, la orden select within 3. Son los siguientes: His, Phe, Trp y Tyr. Los grupos predefinidos RasMol protein y nucleic diferencian entre los dos posibles ejes. De otra manera, utiliza el algoritmo DSSP como lo hace la orden structure.
Normalmente contiene agua, cofactores y otros disolventes y ligandos. Este grupo es equivalente a las expresiones de RasMol " a,c,g,t " y " purine or pyrimidine ". Son las bases adenosina and guanosina A y G respetivamente. De otra forma utiliza el algoritmo DSSP como lo hace la orden structure. Los grupos RasMol predefinidos protein y nucleic sirven para distinguir entre las dos formas de cadenas laterales.
Por ejemplo, si escribe el rachivo ' gris. En el resto de los casos se dispone de 8 colores. Este esquema de color es parecido al esquema shapely. Los valores altos se colorean en azul positivo y los mas bajos en rojo negativo. Este esquema no asigna a cada carga un valos fijo, si no que en base al mayor y menor valor de carga, interpola colores aproximadamente del azul al rojo. Por ello el verde no puede ser considerado como sin carga neta. La diferencia entre los esquemas ' charge ' y ' temperature ' es el orden de colores, el incremento de temperatura lleva del azul al rojo, mientras que el incremento de carga lleva del rojo al azul.
El esquema de color de RasMol cpk se basa en los colores de los populares modelos de bolas desarrollados por Corey, Pauling y mas tarde mejorado por Kultun. Cada una de las cadenas aparece como un espectro desde el azul al rojo pasando por el verde, el amarillo y el naranja.
Esta orden instruye a RasMol para usar solo residuos no hetero en la escala de colores de grupo. Los valores altos se colorean en azul y los mas bajos en rojo. Este esquema se basa en los "Shapely Models" de Bob Fletterick. Es parecido al esquema de color amino.
La diferencia entre los esquemas de colores temperature y charge consiste en que los valores de temperatura que aumentan van desde el azul al rojo; mientras que los valores de carga en aumento del rojo al azul. El esquema de colores user usuario de RasMol permite a este programa usar el esquema de colores almacenado en el archivo PDB. Este tipo de esquema de colores fue introducido por Belhadj-Mostefa y Milner-White.
La base de datos Protein Data Bank is un archivo de datos de estructuras macromoleculares basado en ordenador. Los archivos PDB consisten en registros 80 caracteres cada uno. Usando el modelo de tarjeta perforada, las columnas 1 a 6 contienen un identificador del tipo de registro, las columnas 7 a 70 contienen datos.
Masullo, C. Liotto 2. Pozhvanov 2. Todorov 2. In July , Dr. Eric Martz of the University of Massachusetts made further revisions. Portions of the 2. Changes were made in August for RasMol version 2.
Bernstein and Frances C.
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