Procedural Thinking - Composed of many steps
Abstranct Thinking - 2 apples equavalent to number 2
Sytematic Debug - Identify and locate program
Tech Empathy - Take an idea and break it down into steps
Tags and Elements - HTML documents are made of HTML eleandents. An element is a tag string. When writing HTML we tell browsers the type of each element by using HTML tags.
Inline vs Block Elements
HTML elements are either inline or block. Block elements form an invisible box around the contents
Anchor Tag used for links. Ex: ref="www.att.com"b = bold, em = emphasis or italics
Attribute Tag ATTR = "value
Image Tag is used to link to images
br = Break Tag is a Void Tag is used to br
br = Break Tag is a Void Tag is used to break to a new line
Paragraph Tag = br
Container Elements
Span Element - an inline element and does not break to a new line.
DIV Element - a block Element and breaks to a new line.
CSS Element - Class (used to add a certain style to the text)


1992-1998 by Roger Sayle
<EMAIL_ADDRESS>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.
The commands/keywords currently recognised by RasMol are given below.
Backbone Background Centre Clipboard Colour Connect CPK Dots Define Echo Exit HBonds Help Label Load Print Quit Renumber Reset Restrict Ribbons Rotate Save Script Select Set Show Slab Source Spacefill SSBonds Strands Structure Trace Translate Wireframe Write Zap Zoom
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 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 colour backbone command.
The reserved work backbone is also used as a predefined set and as a parameter to the set hbond and set ssbond commands. The RasMol command trace is synonymous with the command backbone.
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.
The background command is synonymous with the RasMol set background command.
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.
Syntax: clipboard
The RasMol clipboard command places a copy of the currently displayed image on the local graphics `clipboard'. Note: this command is not yet supported on UNIX or VMS machines. It is intended to make transfering images between applications easier under Microsoft Windows or on an Apple Macintosh.
When using RasMol on a UNIX or VMS system this functionality may be achieved by generating a raster image in a format that can be read by the receiving program using the RasMol write command.
Syntax: colour {<object>} <colour> color {<object>} <colour>
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 help colours will give a list of all the predefined colour names recognised by RasMol.
Allowed objects are
atoms,
bonds,
backbone,
ribbons
labels
dots,
hbonds,
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 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 connect).
Atom
objects can also be coloured by
cpk,
amino,
chain,
group,
shapely,
structure,
temperature
charge
and
user. Hydrogen bonds can also be coloured by
type
and dot surfaces can also be coloured by
electrostatic potential.
For more information type
help colour
Syntax: connect {<boolean>}
The RasMol connect 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 connect false uses an extremely fast heuristic algorithmm that is suitable for determing bonding in large bio-molecules such as proteins and nucleic acids. The command connect true 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 load command.
Syntax: define <identifier> <expression>
The RasMol define 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 expression defining them depends on the current transformation and representation of the molecule.
Syntax: dots {<boolean>} dots <value>
The RasMol dots 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 dots on deletes any existing dot surface and generates a dots surface around the currently selected atom set with a default dot density of 100. The command dots off 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 surface is generated. The colour of the whole dot surface may be changed using the colour dots command.
Syntax: echo {<string>}
The RasMol echo command is used to display a message in the RasMol command/terminal window. The string parameter may optionally be delimited in double quote characters. If no parameter is specified, the echo command displays a blank line. This command is particularly useful for displaying text from within a RasMol script file.
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.
Syntax: help {<topic> {<subtopic>}} ? {<topic> {<subtopic>}}
The RasMol help command provides on-line help on the given topic.
Syntax: label {<string>} label <boolean>
The RasMol label 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 character specifying the property to be displayed (similar to C's printf syntax). 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 label off. By default, if no string is given as a parameter RasMol uses labels appropriate for the current molecule. RasMol uses the label "%n%r:%c.%a" if the molecule contains more than one chain, "%e%i" if the molecule has only a single residue (a small molecule) and "%n%r.%a" otherwise.
The colour of each label may be changed using the colour label 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 set fontsize command.
The following table lists the current expansion specifiers:
%a Atom Name %b %t B-factor/Temperature %c %s Chain Identifier %e Element Atomic Symbol %i Atom Serial Number %n Residue Name %r Residue Number
Syntax: load {<format>} <filename>
Load a molecule co-ordinate file into RasMol2. Valid molecule file formats are pdb (Brookhaven Protein Databank), mdl (Molecular Design Limited's MOL file format), alchemy (Tripos' Alchemy file format), mol2 (Tripos' Sybyl Mol2 file format), charmm (CHARMm file format) or xyz (MSC's XMol XYZ file format). If no file format is specified, pdb 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 zap command.
The load 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 connect command.
Syntax: print
The RasMol print 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 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 functionality may be achieved by either generating a PostScript file using the RasMol write ps or write vectps commands and printing that or generating a raster image file and using a utility to dump that to the local printer.
Syntax: quit exit
Exit from the RasMol program. The RasMol commands exit and quit are synonymous.
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.
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.
Syntax: restrict {<expression>}
The RasMol restrict 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 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-selected region.
Type "help expression" for more information on RasMol atom expressions.
Syntax: ribbons {<boolean>} ribbons <value>
The RasMol ribbons command displays the currently loaded protein or nucleic acid as a smooth solid "ribbon" 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 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 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 structure command. This command is similar to the RasMol command strands which renders the biomolecular ribbon as parallel depth-cued curves.
Syntax: rotate <axis> {-} <value>
Rotate the molecule about the specified axis. Permited values for the axis parameter are "<tt>x</tt>", "<tt>y</tt>" and "<tt>z</tt>". 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.
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. The distinction between this command and the RasMol write command has been dropped. The only difference is that without a format specifier the save command generates a PDB file and the write command generates a GIF image.
Syntax: script <filename>
The RasMol script command reads a set of RasMol commands 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 maximum "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 echo command.
The most common way to generate a RasMol script file is to use the write script or write rasmol commands to output the sequence of commands that are needed to regenerate the current view, representation and colouring of the currently displayed molecule.
The RasMol command source is synonymous with the script command.
Syntax: select {<expression>}
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 select 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 select all. The behaviour of the select command without any parameters is determined by the RasMol hetero and hydrogen parameters.
Type "help expression" for more information on RasMol atom expressions.
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.
Ambient Axes Background BondMode BoundBox Display FontSize HBonds Hetero HourGlass Hydrogen Kinemage Menus Mouse Radius Shadow SlabMode Solvent Specular SpecPower SSBonds Strands UnitCell VectPS
Syntax: show information show sequence show symmetry
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.
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. 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.
Syntax: spacefill {<boolean>} spacefill temperature spacefill user spacefill <value>
The RasMol spacefill 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, spacefilll true, the default, represents each atom as a sphere of van der Waals radius. The command spacefill off 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 temperature 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 user option allows the radius of each spheres to be specified by additional lines in the molecule's PDB file using Raster 3D's COLOR record extension.
The RasMol command cpk is synonymous with the spacefill command.
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.
Syntax: strands {<boolean>} strands <value>
The RasMol strands 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 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 colour of the central and outermost strands may be coloured independently using the colour ribbon1 and colour ribbon2 commands respectively. The number of strands in the ribbon may be altered using the RasMol set strands 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 secondary structure assignment is either from the PDB file or calculated using the DSSP algorithm as used by the structure command. This command is similar to the RasMol command ribbons which renders the biomolecular ribbon as a smooth shaded surface.
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, strands and turns found.
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 "<tt>x</tt>", "<tt>y</tt>" and "<tt>z</tt>". Displacement values must be between -100 and 100 which correspond to moving the current molecule just off the screen. A positive "<tt>x</tt>" displacement moves the molecule to the right, and a positive "<tt>y</tt>" displacement moves the molecule down the screen. The pair of commands translate x 0 and translate y 0 centres the molecule on the screen.
Syntax: wireframe {<boolean>} wireframe <value>
The RasMol wireframe 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 wireframe or wireframe on. 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 colour bonds command.
Syntax: write {<format>} <filename>
Write the current image to a file in a standard raster format. Currently supported image file formats include "gif" (Compuserve GIF), "ppm" (Portable Pixmap), "ras" (Sun rasterfile), "ps" and "epsf" (Encapsulated PostScript), "monops" (Monochrome Encapsulated PostScript), "bmp" (Microsoft bitmap) and "pict" (Apple PICT). 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.
The distinction between this command and the RasMol save command has been dropped. The only difference is that without a format specifier the save command generates a PDB file and the write command generates a GIF image.
Syntax: zap
Deletes the contents of the current database and resets parameter variables to their initial default state.
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 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 500.
A complete list of internal parameter names is given below.
Ambient Axes Background BondMode BoundBox Display FontSize HBonds Hetero HourGlass Hydrogen Kinemage Menus Mouse Radius Shadow SlabMode Solvent Specular SpecPower SSBonds Strands UnitCell VectPS
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.
Syntax: set axes <boolean>
The RasMol axes parameter controls the display of orthogonal co-ordinate axes on the current display. The co-ordinate 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 the the commands set boundbox and set unitcell that display the bounding box and the crystallographic unit cell respectively.
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.
The command set background is synonymous with the RasMol command background.
Syntax: set bondmode and set bondmode or
The RasMol set bondmode command controls the mechanism used to select individual bonds. 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.
Syntax: set boundbox <boolean>
The RasMol boundbox 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 set boundbox command is similar the the commands set axes and set unitcell that display orthogonal co-ordinate axes and the bounding box respectively.
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 command is typically only used by external Graphical User Interfaces (GUIs).
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. his parameter is similar to the RasMol ssbonds parameter.
Syntax: set fontsize {<value>}
The RasMol set fontsize command is used to control the size of the characters that form atom labels. This value corresponds to the height of the displayed character in pixels. The maximum value of fontsize is 32 pixels, and the default value is 8 pixels high. 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.
Syntax: set hetero <boolean>
The RasMol hetero parameter is used to modify the `default' behaviour of the RasMol select command, i.e. the behaviour of select without any parameters. When this value is false, the default select region does not include an 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.
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.
Syntax: set hydrogen <boolean>
The RasMol hydrogen parameter is used to modify the `default' behaviour of the RasMol select command, i.e. the behaviour of select without any parameters. When this value is false, the default select region does not include any hydrogen or deuterium 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.
Syntax: set kinemage <boolean>
The RasMol set kinemage command controls the amount of detail stored in a Kinemage output file generated by the RasMol write kinemage command. The output kinemage files are intended to be displayed by David Richardson's Mage program. set kinemage false, the default, only stores the currently displayed representation in the generated output file. The command set kinemage true, generates a more complex Kinemage that contains both the wireframe and backbone representations as well as the co-ordinate axes, bounding box and crystal unit cell.
Syntax: set menus <boolean>
The RasMol set menus command enables the canvas window's menu buttons or menu bar. This command is typically only used by graphical user interfaces or to create as large as image as possible when using Microsoft Windows.
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.
Syntax: set radius {<value>}
The RasMol set radius command is used to alter the behaviour of the RasMol dots command depending upon the value of the solvent parameter. When solvent is true, the radius parameter controls whether a true van der Waal's 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 it true VdW value. When the value of solvent is true, 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 solvent and changing solvent resets radius to its new default value.
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.
Syntax: set slabmode <slabmode>
The RasMol slabmode parameter controls the rendering method of objects cut by the slabbing (z-clipping) plane. Valid slabmode parameters are "<tt>reject</tt>", "<tt>half</tt>", "<tt>hollow</tt>", "<tt>solid</tt>" and "<tt>section</tt>".
Syntax: set solvent <boolean>
The RasMol set solvent command is used to control the behaviour of the RasMol dots command. Depending upon the value of the solvent parameter, the dots command either generates a van der Waal's or a solvent acessible 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 Waal's 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 1.2 Angstroms (or 300 RasMol units).
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.
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.
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. his parameter is similar to the RasMol hbonds parameter.
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.
Syntax: set unitcell <boolean>
The RasMol unitcell 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 show symmetry display details of the crystal's space group and unit cell axes. The set unitcell command is similar the the commands set axes and set boundbox that display orthogonal co-ordinate axes and the bounding box respectively.
Syntax: set vectps <boolean>
The RasMol vectps parameter is use to control the way in which the RasMol write command generates vector PostScript output files. The command set vectps on 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 set vectps off
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 "<tt>&</tt>", "<tt>|</tt>" and "<tt>!</tt>" 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!
Examples: backbone and not helix within( 8.0, ser70 ) not (hydrogen or hetero) not *.FE and hetero 8, 12, 16, 20-28 arg, his, lys
The following table gives some useful examples of RasMol atom expressions.
Expression Interpretation * All atoms cys Atoms in cysteines hoh Atoms in heterogeneous water molecules as? Atoms in either asparagine or aspartic acid *120 Atoms at residue 120 of all chains *p Atoms in chain P *.n? Nitrogen atoms cys.sg Sulphur atoms in cysteine residues ser70.c? Carbon atoms in serine-70 hem*p.fe Iron atoms in the Heme groups of chain P
RasMol primitive expressions are the fundamental building blocks of atom expressions. 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 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 serine 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.
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 anisotropic temperature value.
The equality operator is denoted either "<tt>=</tt>" or "<tt>==</tt>". The inequality operator as either "<tt><></tt>", "<tt>!=</tt>" or "<tt>/=</tt>". The ordering operators are "<tt><</tt>" for less than, "<tt><=</tt>" for less than or equal to, "<tt>></tt>" for greater than, and "<tt>>=</tt>" for greater than or equal to.
Examples: resno < 23 temperature >= 900 atomno == 487
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 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 within expressions.
For example, the command select within(3.2,backbone) selects any atom within a 3.2 Angstrom radius of any atom in a protein or nucleic acid backbone. Within expressions are particularly useful for selecting the atoms around an active site.
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 select oxygen is equivalent to the command select elemno=8.
AT Acidic Acyclic Aliphatic Alpha Amino Aromatic Backbone Basic Bonded Buried CG Charged Cyclic Cystine Helix Hetero Hydrogen Hydrophobic Ions Large Ligand Medium Neutral Nucleic Polar Protein Purine Pyrimidine Selected Sheet Sidechain Small Solvent Surface Turn Water
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"
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)"
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"
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"
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.
This set contains all the atoms contained in amino acid residues. This is useful for distinguishing the protein from the nucleic acid and heterogeneous atoms in the current molecule database.
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"
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"
The predefined set mainchain is synonymous with the set backbone.
The set of basic amino acids. These are the residue types Arg, His and Lys. All amino acids are classified as either acidic, basic or neutral. This set is equivalent to the RasMol atom expressions "arg, his, lys" and "amino and not (acidic or neutral)"
This set contain all the atoms in the current molecule database that are bonded to atleast one other atom.
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"
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"
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"
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"
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"
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 predefined set should not be confused with the predefined set alpha which contains the alpha carbon atoms of a protein.
This set contains all the heterogeneous 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 hetero atoms are classified as either ligand or solvent atoms. These heterogeneous solvent atoms are further classified as either water or ions.
This predefined set contains all the hydrogen and deuterium atoms of the current molecule. This predefined set is equivalent to the RasMol atom expression "elemno=1"
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"
This set contains all the heterogeneous phosphate and sulphate ions in the current molecule data file. A large number of these ions are sometimes associated with protein and nucleic acid structures determined by X-ray crystallography. These atoms tend to clutter an image. All hetero atoms are classified as either ligand or solvent atoms. All solvent atoms are classified as either water or ions.
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)"
This set contains all the heterogeneous cofactor and ligand moieties that are contained in the current molecule data file. At this set is defined to be all hetero atoms that are not solvent atoms. Hence this set is equivalent to the RasMol atom expression "hetero and not solvent"
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)"
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)"
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 purine or pyrimidine. This set is equivalent to the RasMol atom expressions "a,c,g,t" and "purine or pyrimidine"
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"
The set of all atoms in proteins. This consists of the RasMol predefined set amino and common post-translation modifications.
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"
The set of pyrimidine nucleotides. These are the bases cytidine and thymidine (C and T respectively). All nucleotides are either purines or pyrimidines. This set is equivalent to the RasMol atom expressions "c,t" and "nucleic and not pyrimidine"
This set contains the set of atoms in the currently selected region. The currently selected region is defined by the preceding select or restrict command and not the atom expression containing the selected keyword.
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.
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"
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)"
This set contains the solvent atoms in the molecule co-ordinate file. These are the heterogeneous water molecules, phosphate and sulphate ions. All hetero atoms are classified as either ligand or solvent atoms. All solvent atoms are classified as either water or ions. This set is equivalent to the RasMol atom expressions "hetero and not ligand" and "water or ions"
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 accessibility 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"
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.
This set contains all the heterogeneous 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. All hetero atoms are classified as either ligand or solvent atoms. The solvent atoms are further classified as either water or ions.
blue [0,0,255] black [0,0,0] cyan [0,255,255] green [0,255,0] greenblue [46,139,87] magenta [255,0,255] orange [255,165,0] purple [160,32,240] red [255,0,0] redorange [255,69,0] violet [238,130,238] white [255,255,255] yellow [255,255,0]
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 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 shapely scheme.
ASP,GLU bright red [230,10,10] CYS,MET yellow [230,230,0] LYS,ARG blue [20,90,255] SER,THR orange [250,150,0] PHE,TYR mid blue [50,50,170] ASN,GLN cyan [0,220,220] GLY light grey [235,235,235] LEU,VAL,ILE green [15,130,15] ALA dark grey [200,200,200] TRP pink [180,90,180] HIS pale blue [130,130,210] PRO flesh [220,150,130]
The RasMol chain colour scheme assigns each macromolecular chain a unique colour. This colour scheme is particularly useful for distinguishing the parts of multimeric structure or the individual `strands' of a DNA chain.
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. The assignment of element type to colours is given below.
Carbon light grey Chlorine green Oxygen red Bromine, Zinc brown Hydogen white Sodium blue Nitrogen light blue Iron purple Sulphur yellow Calcium, Metals dark grey Phosphorous orange Unknown deep pink
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 heterogeneous molecules associated with it, the macromolecule may not be drawn in the full `range' of the spectrum.
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.
The RasMol structure 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 determined using Kabsch and Sander's DSSP algorithm. The RasMol structure command may be used to force DSSP's structure assignment to be used.
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.
The difference between the temperature and charge colour schemes is that increasing temperature values proceed from blue to red, whereas increasing charge valuse go from red to blue.
The RasMol charge 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 charge and temperature colour schemes is that increasing temperature values proceed from blue to red, whereas increasing charge valuse go from red to blue.
If the charge/temperature field stores reasonable values it is possible to use the RasMol colour dots potential command to colour code a dot surface (generated by the dots command) by electrostatic potential.
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 introduced by David Bacon's Raster3D program.
The RasMol type colour scheme applies only to hydrogen bonds, hence is used in the command "colour hbonds type" 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).
Offset Colour Triple +2 white [255,255,255] +3 magenta [255,0,255] +4 red [255,0,0] +5 orange [255,165,0] -3 cyan [0,255,255] -4 green [0,255,0] default yellow [255,255,0]
The RasMol potential colour scheme applies only to dot surfaces, hence is used in the command "colour dots potential" 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 colour charge command. Like the charge colour scheme low values are blue/white and high values are red. The table below shows the static assignment of colours using a dielectric constant value of 10.
25 < V red [255,0,0] 10 < V < 25 orange [255,165,0] 3 < V < 10 yellow [255,255,0] 0 < V < 3 green [0,255,0] -3 < V < 0 cyan [0,255,255] -10 < V < 3 blue [0,0,255] -25 < V < -10 purple [160,32,240] V < -25 white [255,255,255]


The header tag is supported as well.
Even more awesome.


Situated on the southern tip of the island, this town is regarded as one of the most attractive on Corsica. It is however reported to be very expensive, with over-zealous Customs (see comment below).
Position 41°23'N, 09°09'E (Harbour entrance)
It has a large number of visitors' berths but can get very crowded in the season.
Beware of the ground chains in the anchorage.
Good marina and recommended as the best harbour in Corsica.
Last updated March 2015.


Solar North Tool
Set model north direction.
Tool Operation
Click to select reference point
Click to select north direction.
Extension Warehouse


Pompeo says 'did not see' Sondland's testimony, proud of U.S. policy on Ukraine
BRUSSELS (Reuters) - U.S. Secretary of State Mike Pompeo said on Wednesday he did not watch a testimony from European Union Ambassador Gordon Sondland in the impeachment inquiry of President Donald Trump and that he was proud of American policy in Ukraine.
“I didn’t see a single thing ... I was working, I was in meetings all day,” Pompeo told reporters after a NATO foreign ministers’ meeting. “I haven’t had a chance to see any of that testimony.”
Asked if he was considering recusing himself from decisions on documents provided to the U.S. Congress, he said: “I am not going to recuse myself from this. I know precisely what American policy was with respect to Ukraine, I was working on it and I am terribly proud of what we accomplished.”


This is a placeholder for an embedded web app that the Omega's node server could expose to a mobile client. The only function supported by this placeholder is a button for shutting down the Omega device.


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(not really delays anymore)
If you are looking for the precise distance between the frozen edge and the open edge, this can be seen in the footer of the homepage on the client.
Nyzo uses a fixed, 7-second block duration. The "open edge" is the latest block that is available for the blockchain to process. When the cycle is functioning optimally, it will freeze blocks so quickly that there will be a period of waiting between the freezing of a block and the time at which the next block becomes the open edge. This means that the frozen edge will be 0 or 1 blocks behind the open edge at all times.
When the cycle stalls or is not producing blocks quickly enough, the frozen edge can fall far behind the open edge. Previously, such a state would cause new transactions to be delayed by approximately the amount of time between the end timestamp of the frozen edge and the end timestamp of the open edge.
The web wallet was modified to eliminate this delay, and the initial design of the client avoided the delay. When the frozen edge is far behind the open edge, past timestamps are used to compensate. Transactions are always created with timestamps just past the current frozen edge. While this may seem to be an odd manipulation, the mechanics of the blockchain do allow this, and there is nothing to be gained by timestamping transactions with the current timestamp instead of a timestamp in the past.
The ability of the cycle to process transactions in a timely manner is critical to the utility of the system. The verifier-removal process introduced in version 508 helps to ensure the health of the cycle and maintain processing throughput, but we would be naive to assume that stalls or slowdowns will not occur in the future.
Also, any verification of transaction timestamps to prevent the submission of past timestamps would require a consensus process essentially equivalent to the block consensus process. So, the only reasonable way to ensure exclusion of past-timestamped transactions is to freeze blocks quickly.
This does raise the question of what transaction timestamps mean in Nyzo. Simply, a transaction timestamp is the timestamp that the sender of the transaction chose to assign to the transaction, nothing more and nothing less. This timestamp determines block membership. If a transaction is incorporated into the blockchain, then we can trust (as much as we trust the blockchain) that the transaction was produced before or close to the verification timestamp of the block. However, there has never been a guarantee that a transaction included in a block was produced before the end timestamp of that block.
Additionally, this raises the question of what real consequence there is to the blockchain falling behind. This is not a desirable situation, but the state of the blockchain being behind is not the truly undesirable part of the situation; it is only a symptom of prolonged processing difficulties by the cycle. The other issues — consensus delays that reduce blockchain transaction throughput and dropped transactions due to sentinel blocks — these are the problems about which we should truly be concerned.
Finally, this raises a question of whether the concept of a block duration is even useful. The answer to this is a resounding yes, as a fixed block duration allows a default and fallback behavior of timestamping a transaction with its actual creation time. This is an easy-to-understand and easy-to-implement design that allows for fast transaction processing most of the time without requiring those creating transactions to have any knowledge of the current state of the blockchain.


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“I see the children growing up. I see the girls droop and pine in this dreary parsonage, where the winds nip, and the miasma from the churchyard chokes them. I see the handsome promising boy going to the devil—slowly at first, then by strides. As their hope fades from his sisters' faces, he drinks and takes to opium-eating—and worse. He comes home from a short absence, wrecked in body and soul. After this there is no rest in the house. He sleeps in the room with that small, persistent father of his, and often there are sounds of horrible strugglings within it. And the girls lie awake, sick with fear, listening, till their ears grow heavy and dull, for the report of their father's pistol.” — Arthur Quiller-Couch, Noughts And Crosses


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LoginEnter password for Hardware Wallet.LogoutClear password for HWW.Config & ConnectSet the Serial Port communication parameters.Paired Device ({{device.config.name || 'no-name'}})
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ForgetDisconnectDisconnect from Serial Port.RestoreRestore wallet from existing word list.Show SeedShow seed on the Hardware Wallet display.WipeClean-up the wallet. New random seed.HelpView available comands.ConsoleShow the serial port communication messagesEnter Config
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#include <WinCAPICryptoKeyRSA.hpp>
Inheritance diagram for WinCAPICryptoKeyRSA:
The library uses classes derived from this to process RSA keys.
Public Member Functions | |
Constructors and Destructors | |
| WinCAPICryptoKeyRSA (HCRYPTPROV prov) | |
| Create an RSA key. | |
| WinCAPICryptoKeyRSA (HCRYPTPROV prov, HCRYPTKEY k) | |
| Dedicated WinCAPI constructor for a public RSA key. | |
| WinCAPICryptoKeyRSA (HCRYPTPROV prov, DWORD keySpec, bool isPrivate) | |
| Dedicated WinCAPI constructor for a private RSA key. | |
| virtual | ~WinCAPICryptoKeyRSA () |
Key Interface methods | |
| virtual XSECCryptoKey::KeyType | getKeyType () |
| Return the type of this key. | |
| virtual const XMLCh * | getProviderName () |
| Return the WinCAPI identifier string. | |
| virtual XSECCryptoKey * | clone () |
| Replicate key. | |
Mandatory RSA interface methods | |
These classes are required by the library. | |
| virtual void | setOAEPparams (unsigned char *params, unsigned int paramsLen) |
| Set the OAEPparams string. | |
| virtual unsigned int | getOAEPparamsLen (void) |
| Get OAEPparams Length. | |
| virtual const unsigned char * | getOAEPparams (void) |
| Get the OAEPparams. | |
| virtual bool | verifySHA1PKCS1Base64Signature (const unsigned char *hashBuf, unsigned int hashLen, const char *base64Signature, unsigned int sigLen) |
| Verify a SHA1 PKCS1 encoded signature. | |
| virtual unsigned int | signSHA1PKCS1Base64Signature (unsigned char *hashBuf, unsigned int hashLen, char *base64SignatureBuf, unsigned int base64SignatureBufLen) |
| Create a signature. | |
| virtual unsigned int | privateDecrypt (const unsigned char *inBuf, unsigned char *plainBuf, unsigned int inLength, unsigned int maxOutLength, PaddingType padding, hashMethod hm) |
| Decrypt using private key. | |
| virtual unsigned int | publicEncrypt (const unsigned char *inBuf, unsigned char *cipherBuf, unsigned int inLength, unsigned int maxOutLength, PaddingType padding, hashMethod hm) |
| Encrypt using a public key. | |
| virtual unsigned int | getLength (void) |
| Obtain the length of an RSA key. | |
Optional Interface methods | |
Have been implemented to allow interoperability testing | |
| virtual void | loadPublicModulusBase64BigNums (const char *b64, unsigned int len) |
| Load the modulus. | |
| virtual void | loadPublicExponentBase64BigNums (const char *b64, unsigned int len) |
| Load the exponent. | |
WinCAPI Specific Functions | |
| unsigned int | getExponentBase64BigNums (char *b64, unsigned int len) |
| Retrieve the exponent. | |
| unsigned int | getModulusBase64BigNums (char *b64, unsigned int len) |
| Retrieve the modulus. | |
| HCRYPTKEY | importKey (void) |
| Import key and return it. |
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Create an RSA key. Constructor used to create an "empty" RSA key, that the library will later set parameters for the public key within.
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Dedicated WinCAPI constructor for a public RSA key. Create a public RSA key for use in XSEC from an existing HCRYPTKEY
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Dedicated WinCAPI constructor for a private RSA key. Create a public RSA key for use in XSEC from an keySpec
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Replicate key.
Implements XSECCryptoKeyRSA. |
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Retrieve the exponent. Retrieves the exponent in ds:CryptoBinary encoded format
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Return the type of this key. For RSA keys, this allows people to determine whether this is a public key, private key or a key pair Reimplemented from XSECCryptoKeyRSA. |
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Obtain the length of an RSA key.
Implements XSECCryptoKeyRSA. |
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Retrieve the modulus. Retrieves the modulus in ds:CryptoBinary encoded format
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Get the OAEPparams.
Implements XSECCryptoKeyRSA. |
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Get OAEPparams Length.
Implements XSECCryptoKeyRSA. |
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Return the WinCAPI identifier string.
Implements XSECCryptoKey. |
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Import key and return it. Retrieves the RSA key as HCRYPTKEY
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Load the exponent. Load the exponent from a Base64 encoded string param b64 A buffer containing the encoded string param len The length of the data in the buffer Implements XSECCryptoKeyRSA. |
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Load the modulus. Load the modulus from a Base64 encoded string param b64 A buffer containing the encoded string param len The length of the data in the buffer Implements XSECCryptoKeyRSA. |
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Decrypt using private key. The library will call this function to decrypt a piece of cipher text using the private component of this key.
Implements XSECCryptoKeyRSA. |
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Encrypt using a public key. The library will call this function to encrypt a plain text buffer using the public component of this key.
Implements XSECCryptoKeyRSA. |
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Set the OAEPparams string. By default, the library expects crypto implementations to perform OAEP padding with no params. This call allows the library (or user) to set a params value prior to an encrypt/decrypt operation.
Implements XSECCryptoKeyRSA. |
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Create a signature. The library will call this function to create a signature from a pre-calculated digest. The output signature will be Base64 encoded such that it can be placed directly into the XML document
Implements XSECCryptoKeyRSA. |
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Verify a SHA1 PKCS1 encoded signature. The library will call this function to validate an RSA signature The standard by default uses SHA1 in a PKCS1 encoding.
Implements XSECCryptoKeyRSA. |


Ryan Womack is Data Librarian at Rutgers University.
pronouns: he/him
e-mail:
rwomack at rutgers.edu
(Rutgers)
or
ryan at ryanwomack.com
(non-Rutgers)
Appointments:
meet with me
Youtube:
librarianwomack
Mastodon:
<EMAIL_ADDRESS>Blog:
right here on this site
github:
ryandata
ORCID:
0000-0003-4873-4268
RSS:
RSS feed for blog
Curriculum Vitae
Librarianship
Since 2013, I serve as Data Librarian for the New Brunswick Libraries, part of Rutgers University Libraries. Prior to this, I was Data and Economics Librarian, and prior to that, Business and Economics Librarian. Since 1999, I have been a member of the library faculty of Rutgers University-New Brunswick. I was granted tenure and promoted to the rank of Librarian II in 2005. In 2019, I was promoted to the rank of Librarian I (equivalent to Full Professor). I hold an M.A. in Economics from the University of Pennsylvania, an M.S. in Library Science from the University of North Carolina-Chapel Hill, and an M.S. in Statistics and Biostatistics from Rutgers University-New Brunswick.
As Data Librarian for Rutgers-New Brunswick, I am responsible for Data Services, including outreach and training for data, assisting students and faculty, acquisition of data sources, development of research guides, and providing support for quantitative research across a range of disciplines. I led the development of the Graduate Specialist Program, hiring Rutgers-NB graduate students to teach workshops and provide consultations in advanced research methods, including Python, R, and other data science topics. I am serving from 2022 to 2025 as the Head of the New Brunswick Libraries Research Services Unit. I am particularly interested in developing and supporting data literacy and statistical literacy.
I am the subject specialist for and liaison to the Department of Economics, and the Department of Agricultural, Food, and Resource Economics. I manage the Libraries' collections, give instructional sessions, and help researchers and students locate information in these disciplines. I am also the New Brunswick Libraries Point of Contact for Government Documents and Statistical Data Services.
Some occasional thoughts about data and other things are at my blog here. I also maintain the Libraries research guide for Data and for Economics.
A current focus for me is the development of useful guides to data and statistical resources related to Mongolia and the countries of Central Asia (Kazakhstan, Kyrgzstan, Tajikistan, Turkmenistan, Uzbekistan). The Central Asia and Mongolia Gender Data Portal (CAMGDP) exemplifies this.
Scholarship
This page highlights major publications. See the CV links above for complete and current publication details.
Selected Peer-reviewed Articles
- Ryan Womack, “ARL Libraries and Research: Correlates of Grant Funding”, The Journal of Academic Librarianship, volume 42, issue 4, 2016.
- Ryan Womack, “Research Data in Core Journals in Biology, Chemistry, Mathematics, and Physics”, PLoS ONE, volume 10, issue 12, 2015.
- Ryan Womack, “Data Visualization and Information Literacy”, IASSIST Quarterly, volume 38, issue 1, 2014, pp. 12-17.
- Ryan Womack, “The Orientation and Training of New Librarians for Business Information”, Journal of Business and Finance Librarianship, volume 13, issue 3, 2008, pp. 217-226. Preprint in RUcore
- Ryan Womack, “Information Intermediaries and Optimal Information Distribution”, Library and Information Science Research, vol. 24, no. 2, 2002, pp. 129-155. Preprint in RUcore
Selected Additional Publications
- Mei Ling Lo, Li Sun, Ryan Womack, Connie Wu, and Tao Yang. “Celebrating Diversity, Welcoming the World: Developing Chinese Webpages at Rutgers University Libraries”, 2009. CALA Occasional Papers Series, no. 5, June 2009.
- Ryan Womack (Editor), Success by the Numbers: Statistics for Business Development. Chicago: Reference and User Services Association of the American Library Association, 2005. (RUSA Occasional Paper, number 28).
- Ryan Womack, “High Speed, High Price, High Demand: Business Internet Resources and Databases in American Academic Libraries”, Proceedings of Central Asia 2002: Internet and Library, Information Resources in Science, Culture, Education, and Business, Bukhara, Uzbekistan, October 2002, pp. 37-41.
Selected Presentations
- “The Central Asia and Mongolia Gender Data Portal”, IASSIST Annual Conference, Philadelphia, PA, May 31, 2023. More information
- “Addressing Diversity in Data through the work of Graduate Specialists”, IASSIST Annual Conference (Hybrid), Gothenburg, Sweden, June 8, 2022.
- “From Pilot to JetStream: Building training pathways and collaboration in data science and digital humanities through the Library”, IASSIST Annual Conference (Virtual), May 20, 2021. (postponed from 2020 due to COVID-19). Short, Medium, and Long versions of the talk.
- “Big Data, Data Visualization, and Reproducible Research”, Mongolian University of Science and Technology, Ulaanbaatar, Mongolia, May 12, 2017.
- “Data in Libraries: Data Processing and Visualization”, Reference and User Services Association of the American Library Association, online, , May 4, 2017 [repeated November 2, 2017].
- “Putting Reproducibility into Practice: Workflows and Case Studies”, Rutgers Workshop on Reproducibility in Experimental and Computational Science, Piscataway, NJ, October 10, 2016.
- “(a bit about) Data Visualization”], ICPSR Biennial Meeting, University of Michigan, Ann Arbor, October 2, 2015.
Selected Workshops
- “A Short Course in Multivariate Statistical Methods with R/Олон хэмжээст статистикийн богино хэмжээний сургалт R программ дээр”, one-week mini-course, Mongolian University of Life Sciences [Хөдөө аж ахуйн их сургуул], Ulaanbaatar, Mongolia, February 26-March 2, 2018.
- “Data Literacy for All, with R”, IASSIST Annual Conference, Lawrence, Kansas, May 23, 2017 [repeated May 29, 2018 IASSIST Annual Conference, Montréal, Canada].
- “Topics in Data Science/Өгөгдлийн шинжлэх ухаан [Data Visualization, Big Data, Reproducible Research, and Data Literacy]”, National Statistics Office of Mongolia, Ulaanbaatar, Mongolia, May 8-9, 2017. PDF available at https://doi.org/doi:10.7282/T3CF9SS7.
- Ryan Womack, “Hands-On Big Data”, IASSIST Annual Conference, Minneapolis, Minnesota, June 2, 2015.
- “Data Visualization and R”, IASSIST Annual Conference, Cologne, Germany, May 29, 2013 [repeated June 3, 2014, IASSIST Annual Conference, Toronto, Canada].
- R workshops at Rutgers are offered to students and faculty across the University, from a wide range of science and social science departments. Topics include statistical functions, graphics, data manipulation, data visualization, time series, and survival analysis. See my R page for workshop materials.
Service
I am an active member of IASSIST (the
International Association for Social Science Information Service and
Technology), currently serving as Member at Large for the USA. I served as Secretary of the Association from 2015 to
2019.
On the national level, I was once active in the Business Reference and
Services Section (BRASS) of the American Library
Association, including a term as Chair.
See my CV for further details of local activity.
Last updated 2023-05-12


Data Source Class Logic
Over this past weekend, we did a near complete rewrite of how we handle data sources. Previously, there was a single DataSource
parent class from which we derived our three subclasses, each representing a different type of data, and then a plugin through which the user could implement their own data source and override our basic methods.
DataSource (baseclass)
--> WebDataSource (subclass for specific data type)
--> Plugin (contains user overrides)
Through this method, the base class would specify the vast majority of the logic. The subclass then inherits abstractmethods
which tell the program what to do with the data source, and tweaks them to its own specifications, and from there the user receives them and alters them further to meet their needs (i.e. getting specified data from a webscrape).
This method introduced several issues:
- How do we inform the base class constructor of the user overrides?
- Each function is implemented three times, each time more focused than the last
- If the user needs to override the functions anyway, why implement the generalized functions at all, rather than just implementing the specific ones at the user end?
It was overcomplicated, to put it simply. We only needed to do a handful of tasks: fetch the data, clean it up, and insert it into the database, and run all of that automatically on a schedule.
We’ve now completely removed the tangle of classes, keeping only the base DataSource
class. Methods are defined once within the user files; they can still be overridden as necessary, but serve as a base function to fall back on. Each data type on our end is now treated the same, and it will be up to the user to prepare that data to be collected, rather than build functions to identify the datasource and what to do with it.


{% load static %}
Government Engineering College Bilaspur, is a provider of University level technical education and research in Chhattisgarh state. The institute is is affiliated to Chhattisgarh Swami Vivekanand Technical University (CSVTU), Bhilai and approved by All India Council for Technical Education (AICTE), Delhi. Since its inception in 1964, college is a dynamic, fast growing educational institution. College provides a safe and supportive environment to foster the academic development and welfare of students. Imbibed with the message of “Yogah Karmasu Kaushalam”, the institute is offering a flexible and real world based approach in education. GEC Bilaspur offers 7 courses for Graduation i.e., Civil Engineering, Mechanical Engineering, Electrical Engineering, Mining Engineering, Electronics and Telecommunications, Computer Science and Engineering, and Information Technology.
The city of Bilaspur is a main junction on Howrah-Mumbai rail route of South Eastern Central railway. The distance of the institution from railway station is 10 km and the nearest airport is Swami Vivekanand Airport Raipur (115km). This institute is located on Korba road amidst the peaceful, lush green and natural region of Koni village. It is well connected by Rail and Roadways to other main cities.
Explore our Website.


Around the middle of July 2017 was big news: The Bitcoin developers agreed on the need to update the protocol using the SegWit2x technology (Segregated Witness). Such a solution was proposed by the Bitcoin Core development team and it was supported by the largest mining pools from China – they agreed to update the protocol, which promised to improve the performance of the entire network, but some of the large mining companies supported the division.
As a result of the hard fork, there was a new coin that is called Bitcoin Cash (BCH). As commented Charles Morris, a representative of NextBlock Global investment company:
"A group of miners who did not like the option using SegWit2x decided to increase the block size of cryptocurrency from 1 MB to 8 MB".
So, on August 1, the BCH was born with a block size of 8 MB. Bitcoin Cash is a cryptocurrency, born as a fork of Bitcoin. Today Bitcoin Cash is one of the largest cryptocurrencies and takes place in Top 5 cryptocurrencies in the world. Bitcoin Cash market capitalization is about $ 2 BLN and its daily volume is about $ 200 MLN. Bitcoin Cash is also one of the value cryptocurrencies, today BCH price is about 125 USD for 1 BCH.
If the hard fork of Bitcoin Cash didn’t happen in 2018, this coin could be even more perspective in new 2019. But today there is the new coin, it’s called Bitcoin SV (BSV) and there was a #HashWars for the advantages of the initial hard fork. BCH price had a hard war with BSV price for the leading position and won it. At this moment BCH price is almost twice that the BSV price.
Bitcoin Cash price was also bigger than today. The max BCH price was $ 4091 at the end of 2017, and its middle price for last years is about $ 400-600, so today it has the potential to grow. But in 2019, several significant news will take place on the cryptocurrency market: The US Securities and Exchange Commission will make another decision on Bitcoin ETF, start the platform for institutional investors Bakkt and Fidelity, and much more, so you should be aware about Bitcoin Cash (BCH) news if you trade it to take a profit.
#1 Wallet Investor Bitcoin Cash Price Prediction
BCH price may spike down to the level of $ 11 by the end of 2019.
#2 Smartereum Bitcoin Cash Price Prediction
In 5 years Bitcoin Cash price will probably be $10.000. Very positibe price forecast for BCH coin.
#3 LongForecast Bitcoin Cash Price Prediction
In December, 2019 the price of BCH will probably be in the level between $51 and $66.
After the launch, Bitcoin Cash set a record for the number of trading platforms, which added BCH to the list of trading pairs. Today, the coin takes a place on all the leading exchanges, this makes the BCH accessible to a wide range of users which has an influence on Bitcoin Cash price.
Supporters of the BCH began to unite even before the Bitcoin hard fork and the official release of the Bitcoin Cash. The advantages of the new algorithm, in which the processing of transactions took four times less time was really attractive for a lot of users. Even today, at a difficult time for the entire industry, the BCH price is still one of the largest on the market. And by the end of the year the price will prbably spike up to the $ 220 in it's value.
In 2018 the BCH news was not too favorable. One of the first disturbing events was the delisting of BCH on the KuCoin and OKEx trading platforms. Official reasons were not voiced, but according to rumors, BCH pairs just turned out to be unpopular.
But according to the high level of capitalization, the BCH name can hardly be forgotten army of fans in the coming 2019 year. It is hard to tell what will happen in the long term because the BCH fundamental technology is inferior to the same Ethereum or EOS. Therefore, experts recommend considering the BCH as a tool for medium-term investments (for the next year and a half).
At the same time the BCH developers plan to provide the technical ability to enjoy the benefits of cryptocurrency to all people on the earth. They plan to develop educational projects and create charitable foundations for third world countries. They are working on mass adoption and provide opportunities for turning into a global cryptocurrency for daily payments which is certainly will have an effect on the Bitcoin Cash price.
To make a good choice of the cryptocurrency wallet you need to know the difference between them. There are 3 types of the cryptocurrency wallets:
Cold wallets download the full node. Custodial wallets store your Private keys in their bases and it theoretically may be hacked. Decentralized wallets store your Private keys in an encrypted manner on your device, so while you own your 12 words you can be sure that your money is under your control.
Atomic Wallet is a decentralized wallet that supports BCH and other 300+ cryptocurrency assets, so you can manage all of your cryptocurrencies on one secure interface.
Manage and exchange Bitcoin Cash in one secure interface of Atomic Wallet with built-in exchange service. Atomic supports over 60 trading pairs for instant exchange with the market rates.