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| Commands:
Using RasTop Menu Commands All Commands Command Ref. Internal Parameters
Atom Expression
Colour Schemes
Atom Sets
RasTop World
Command list:
Add Backbone Background Bond Cartoon
Centre
Clipboard
Copy
Colour
Connect
CPK
Dash
Define
Depth
Dots
Echo
Exit
HBonds
Help
Label
Load
Molecule
Monitor
Pause
Paste
Position
Print
Quit
Refresh
Renumber
Reset
Restrict
Ribbons
Rotate
Save
Scale
Script
Select
Set
Show
Slab
Source
Spacefill
SSBonds
Star
Stereo
Strands
Structure
Trace
Translate
Unbond
Wireframe
Write
Zap
Zoom

Command References

RasMol allows the execution of interactive commands. Each command must be given on a separate line. Keywords are case insensitive and may be entered in either upper or lower case letters. All white space characters are ignored except to separate keywords and their arguments.

In RasTop, commands are either automatically generated by the menu or manually entered in the dialog box opened by click the Edit>Command menu item.

### `` Add

RasTop Specific:

    Syntax:  add <filename>

The RasTop '`add`' command loads an RSM script file into the world. Actual world parameters are used to position the molecule instead of those indicated in the script. Other commands listed thereafter are equally deactivated:

    	centre
    	set axes world
    	set slab
    	set shadow
    	set specular
    	set specpower
    	set shadepower
    	set ambient
    	set background
    	set light
    	set fontsize
    	set fontstroke
    	set stereo
    	set backfade
    	set depthcue
    	reset
    	zap
    	slab
    	depth
    	zoom
    	rotate world
    	rotate all
    	translate world
    	position world
    	scale
    	stereo
    	background
    	light

The '`add`' command preserves the rendering and is used to in script saving.

### `` Backbone

    Syntax:  backbone {<boolean>}
             backbone <value>
             backbone dash

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 parameter in the same way as with 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 Ångstrom or RasMol units. A parameter value of 500 (2.0 Ångstroms) or above results in a "Parameter value too large" error. Backbone objects may be coloured using the RasMol '`colour backbone`' command.

The reserved word backbone is also used as a predefined set ("help sets") and as a parameter to the '`set hbond`' and '`set ssbond`' commands. The RasMol command '`trace`' renders a smoothed backbone, in contrast to '`backbone`' which connects alpha carbons with straight lines.

The backbone may be displayed with dashed lines by use of the '`backbone dash`' command.

### `` Background

    Syntax:  background <colour>

The RasMol '`background`' command is used to set the colour of the "canvas" background. The colour may be given as either a colour name or a comma separated triple of Red, Green and Blue (RGB) components enclosed in square brackets. Typing the command '`help colours`' will give a list of the predefined colour names recognised by RasMol. When running under X Windows, RasMol also recognises colours in the X server's colour name database.

The '`background`' command is synonymous with the RasMol '`set background`' command.

### `` Bond

    Syntax:  bond <number> <number> +
    	bond <number> <number> pick
    	bond rotate {<boolean>}

    RasTop Specific (self-explanatory):

    Syntax:  bond <number> <number> -
    	bond <number> <number> single
    	bond <number> <number> double
    	bond <number> <number> triple
    	bond <number> <number> unbound

The RasMol command 'bond <number> <number> +' adds the designated bond to the drawing, increasing the bond order if the bond already exists. The command 'bond <number> <number> pick' selects the two atoms specified by the atom serial numbers as the two ends of a bond around which the 'rotate bond <angle>' command will be applied. If no bond exists, it is created (RasTop: The bond is not created!).
Rotation around a previously picked bond may be specified by the 'rotate bond <angle>' command, or may also be controlled with the mouse, using the 'bond rotate on/off' or the equivalent 'rotate bond on/off' commands.

### `` Cartoon

    Syntax:  cartoon {<number>}

The RasMol '`cartoon`' command does a display of a molecule '`ribbons`' as Richardson (MolScript) style protein '`cartoons`', implemented as thick (deep) ribbons. The easiest way to obtain a cartoon representation of a protein is to use the '`Cartoons`' option on the '`Display`' menu. The '`cartoon`' command represents the currently selected residues as a deep ribbon with width specified by the command's argument. Using the command without a parameter results in the ribbon's width being taken from the protein's secondary structure, as described in the '`ribbons`' command. By default, the C-termini of beta-sheets are displayed as arrow heads. This may be enabled and disabled using the '`set cartoons`' command. The depth of the cartoon may be adjusted using the '`set cartoons <number>`' command. The '`set cartoons`' command without any parameters returns these two options to their default values.

### `` Centre

    Syntax: centre {all}
    	centre {<expression>} {translate|center}
    	centre [x,y,z]

    RasTop Specific:

    	centre world
    	centre molecule
    	centre origin {translate|center}

The RasMol '`centre`' command defines the point about which the '`rotate`' command and the scroll bars rotate the current molecule. With '`all`' parameter or without a parameter the centre command resets the centre of rotation to 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`' on the command line for more information on RasMol atom expressions or consult the document on atom expressions and the predefined atom sets.

Alternatively the centering may be given as a comma separated triple of [CenX, CenY, CenZ] offsets in RasMol units (1/250 of an Angstrom) from the centre of gravity. The triple must be enclosed in square brackets.
The optional forms 'centre ... translate' and 'centre ... center' may be used to specify use of a translated centre of rotation (not necessarily in the centre of the canvas) or a centre of rotation which is placed at the centre of the canvas. Starting with RasMol 2.7.2, the default is to center the new axis on the canvas.

The RasTop '`centre world`' command translates the entire world and positions the world origin to the center of the canvas. A translation along the z-axis is performed if necessary.

The RasTop '`centre molecule`' command is a shortcut for the command '`centre [0,0,0] translate`', which switches the center to the center of gravity of the molecule without translating the molecule itself.

The RasTop '`centre origin`' command transfers the rotation center to the world origin. This special rotation center is active only when the '`rotate all`' command is 'on' (or the '`rotate molecule`' is 'off'). Applications include cases where we need to rotate a single molecule from a center outside the bounding box, and rotations of molecular assemblies that have some degrees of symmetry.

The RasTop '`centre origin centre`' command transfers the world origin to the actual rotation center; molecules are not translated. Inversely, the '`centre origin translate`' command transfers the rotation center to the world origin. One or more molecules are translated, depending on the state on or off of the '`rotate molecule'` command. These two command are useful to align molecules.

When the '`rotate all`' command is 'on', selection of other molecules does not change the rotation center. On the other hand, the '`rotate molecule on`' command brings automatically the center in the bounding box of the active molecule, by default at the gravity center and without translation.

### `` Clipboard

    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 transferring 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.

RasTop specific:

    Syntax:  clipboard selected
             clipboard position
             clipboard {image}
             clipboard paste

The commands '`clipboard selected`' and '`clipboard position`' generate scripts describing the current selection and the current world position of the molecule. These scripts are copied to the clipboard and are pasted from the clipboard using the command '`clipboard paste`' or more simply '`paste`'. The clipboard format used by RasTop is described in the document file formats.

The command 'clipboard image' is equivalent to the RasMol command 'clipboard'. The keyword 'image' is optional.

### `` Colour

    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 recognized by RasMol or consult the document on colour schemes.

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 to all objects except 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 '`alt`', '`amino`', '`chain`', '`charge`', '`cpk`', '`group`', '`model`', '`shapely`', '`structure`', '`temperature`' or '`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 <colour>`' or consult the document on colour schemes.

RasTop Specific: The world axe colour is accessible by the command '`colour world axes <colour>`'; the command '`colour dots none`' is accepted.

### `` Copy

RasTop specific command.

    Syntax:  copy selected
             copy position
             copy {image}

This command is synonymous to '`clipboard`'.

### `` Connect

    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 a fast heuristic algorithm that is suitable for determining 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 to 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 input 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.

### `` Dash

    Syntax:  {wireframe} dash {<boolean>}
             {wireframe} dash <value>

The RasMol '`dash`' command represents each bond within the selected region of the molecule as a dashed depth-cued vector. Behavior of the 'dash' command follows the '`wireframe`' command.

### `` Define

    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.

Type '`help expression`' on the command line for more information on RasMol atom expressions or consult the document on atom expressions and the predefined atom sets.

### `` Depth

    Syntax:  depth {<boolean>}
             depth <value>

The RasTop '`depth`' command enables, disables or positions the back-clipping plane of the molecule. The program only draws those portions of the molecule that are closer than the clipping plane. Integer values range from 0 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.

This command interacts with the 'slab <value>' command, which clips to the front of a given z-clipping plane. Combinations of slabmode and backclipping slice the molecule if the slab value if superior to the depth value.

RasTop Specific:

    Syntax:  depth world origin
             depth world <value>

The '`depth world origin`' command sends the back-clipping plane at the world origin. The '`depth world <value>`' command moves the plane of value Angstroms (if value if a floating number) or value RasMol units (if value is an integer) relatively to its current position. Future versions of RasMol may not adopt this convention.

### `` Dots

    Syntax:  dots {<boolean>}
             dots <value>

The RasMol '`dots`' command is used to generate a van der Waals' 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 Waals' 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 its closest atom at the time the surface is generated. The colour of the whole dot surface may be changed using the '`colour dots`' command.

### `` Echo

    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.

### `` HBonds

    Syntax:  hbonds {<boolean>}
             hbonds <value>

The RasMol '`hbond`' command is used to represent the hydrogen bonding of the protein molecule's backbone. This information is useful in assessing the protein's secondary structure. Hydrogen bonds are represented as either dotted lines or cylinders between the donor and acceptor residues. The first time the '`hbond`' command is used, the program searches the structure of the molecule to find hydrogen bonded residues and reports the number of bonds to the user. The command '`hbonds on`' displays the selected 'bonds' as dotted lines, and the '`hbonds off`' turns off their display. The colour of hbond objects may be changed by the '`colour hbond`' command. Initially, each hydrogen bond has the colours of its connected atoms.

By default the dotted lines are drawn between the accepting oxygen and the donating nitrogen. By using the '`set hbonds`' command the alpha carbon positions of the appropriate residues may be used instead. This is especially useful when examining proteins in backbone representation.

### `` Help

    Syntax:  help {<topic> {<subtopic>}}
             ? {<topic> {<subtopic>}}

The RasMol '`help`' command provides on-line help on the given topic.

RasTop Specific:

    Syntax:  help HTML {<filename | URL>}

The command '`help HTML`' activates the default browser and points its locator to an HTM-based help file. The '`help HTML <filename>`' command sets the address of the HTML-based help file. This help could be an HTML document residing either locally on the drive or externally on the world wide web. In this last case, the address must be given as an URL (http://www.etc.).

### `` Label

    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 and spacing of the displayed text may be changed using the '`set fontsize`' command. The width of the strokes in the displayed text may be changed using the '`set fontstroke`' 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
>     %m      Single Letter Amino Acid Code
>     %n      Residue Name
>     %r      Residue Number
>     %M      NMR Model Number (with leading "/")
>     %A      Alternate Conformation Identifier
>     	(with leading ";")

### `` Load

    Syntax:  load {<format>} <filename>

Load a molecule coordinate file into RasMol. Valid molecule file formats are '`pdb`' (Protein Data Bank format), '`mdl`' (Molecular Design Limited's MOL file format), '`alchemy`' (Tripos' Alchemy file format), '`mol2`' (Tripos' Sybyl Mol2 file format), '`charmm`' (CHARMm file format), '`xyz`' (MSC's XMol XYZ file format), '`mopac`' (J. P. Stewart's MOPAC file format) or '`cif`' (IUCr CIF or mmCIF file format). If no file format is specified, '`PDB`', '`CIF`', or '`mmCIF`' is assumed by default.

Unlimited number of molecules may be loaded at a time. To select a molecule for manipulation use the RasMol '`molecule <n>`' command. To delete specifically a molecule use the RasMol '`zap molecule`' command.

The '`load`' command selects all the atoms in the molecule, centers 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 fewer bonds than atoms, RasMol determines connectivity using the '`connect`' command. If a default script is available (see '`script default`' command), it will be ran automatically after loading.

The '`load inline`' command also allows the storing of atom coordinates in scripts to allow better integration with WWW browsers. A load command executed inside a script file may specify the keyword '`inline`' instead of a conventional filename. This option specifies that the coordinates of the molecule to load are stored in the same file as the currently executing commands.

Typically this is used in the command '`load pdb inline`', which is followed by a number of RasMol commands terminated by the command '`exit`'. The '`exit`' command terminates execution of the current script and returns control to the command line (or the calling script). This means any lines following '`exit`' are never interpreted by RasMol. These may be used to store atomic coordinates in PDB, CIF or mmCIF file format. One possible use is a standard RasMol script prefix that may be concatenated with an appropriate PDB file on-the-fly.

### `` Molecule

    Syntax:  molecule <number>

Select one of up to n previously loaded molecules for active manipulation. While all molecules may be rotated collectively (see the 'rotate all' command), only one molecule at a time is active for manipulation by the commands which control the details of rendering.

RasTop Specific:

    Syntax:  molecule hide
    	molecule show

The command '`molecule hide`' toggles off the display of a molecule. The molecule remains visible in 'display selected mode' as a dashed wireframe. The command '`molecule show`' toggles back on the display of the molecule

### `` Monitor

    Syntax:  monitor <number>  <number>
             monitor {<boolean>}

The RasMol '`monitor`' command allows the display of distance monitors. A distance monitor is a dashed (dotted) line between an arbitrary pair of atoms, optionally labelled by the distance between them. The RasMol command '`monitor <number> <number>`' adds such a distance monitor between the two atoms specified by the atom serial numbers given as parameters

Distance monitors are turned off with the command '`monitors off`'. By default, monitors display the distance between its two end points as a label at the centre of the monitor. These distance labels may be turned off with the command '`set monitors off`', and re-enabled with the command '`set monitors on`'. Like most other representations, the colour of a monitor is taken from the colour of its end points unless specified by the '`colour monitors`' command.

Distance monitors may also be added to a molecule interactively with the mouse, using the '`set picking monitor`' command. Clicking on an atom results in its being identified on the rasmol command line. In addition every atom picked increments a modulo counter such that, in monitor mode, every second atom displays the distance between this atom and the previous one. The shift key may be used to form distance monitors between a fixed atom and several consecutive positions. A distance monitor may also be removed (toggled) by selecting the appropriate pair of atom end points a second time.

### `` Pause

    Syntax:  pause
             wait

The RasMol '`pause`' command is used in script files to stop the script file for local manipulation by a mouse, until any key is pushed to restart the script file. '`Wait`' is synonymous with '`pause`'. This command may be executed in RasMol script files to suspend the sequential execution of commands and allow the user to examine the current image. When RasMol executes a '`pause`' command in a script file, it suspends execution of the rest of the file, refreshes the image on the screen and allows the manipulation of the image using the mouse and scroll bars, or resizing of the graphics window. Once a key is pressed, control returns to the script file at the line following the '`pause`' command. While a script is suspended the molecule may be rotated, translated, scaled, slabbed and picked as usual, but all menu commands are disabled. The '`pause`' can probably be used most effectively with '`echo`' commands in education pre-scripted demonstrations, where a description of the current image is presented to the user/student. Typically the command before a '`pause`' should be '`echo Press any key to continue`'.

Execution of a script can be cancelled by pressing Control-D or Control-Z (on VAX/VMS, Control-C) while standing at a pause. The command '`set picking none`' disables picking, which avoids the display of spurious messages whilst a script is suspended at a pause.

### `` Position

    Syntax:  position {x <number>} {y <number>} {z <number>}
    	position world {x <number>} {y <number>} {z <number>}

The command '`position`' places molecules relatively to the center of the screen and the world plane. The command '`position world`' places the world relatively to the center of the screen and the world plane. Displacement values for more than one axis may be indicated in the same command and are counted in RU for integer values or angstrom for floating values.

### `` Print

    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, this allows 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.

### `` Quit

    Syntax:  quit
             exit

Exit from the RasMol program. The RasMol commands '`exit`' and '`quit`' are synonymous, except within nested scripts. In that case, '`exit`' terminates only the current level, while '`quit`' terminates all nested levels of scripts.

### `` Refresh

    Syntax:  refresh

The RasMol '`refresh`' command redraws the current image. This is useful in scripts to ensure application of a complex list of parameter changes.

### `` Renumber

    Syntax:  renumber {{-} <value>}

The RasMol '`renumber`' command sequentially numbers the residues in a macromolecular chain. The optional parameter specifies the value of the first residue in the sequence. By default, this value is one. For proteins, each amino acid is numbered consecutively from the N terminus to the C terminus. For nucleic acids, each base is numbered from the 5' terminus to the 3' terminus. All chains in the current database are renumbered and gaps in the original sequence are ignored. The starting value for numbering may be negative.

### `` Reset

RasTop Specific:

With the development of complex transformations such as bond modifications and multiple molecules, the reset command needed more precise specifications. The following is an attempt to explore various reset possibilities. Their definition and action may change in future versions of RasTop.

    Syntax: reset
    	reset molecule
    	reset world
    	reset worlddepth
    	slab
    	depth
    	headlight
    	bonds
    	all

If only one molecule is loaded and the world is not active, the RasTop '`reset`' and '`reset molecule`' commands restore the original viewing transformation and centre of rotation. The scale is set to its 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. All world parameters are reset. This command should not be mistaken for the RasMol '`zap`' command which deletes the currently stored molecule, returning the program to its initial state.

If more than one molecule is loaded, the RasTop '`reset molecule`' command restores the original parameter of the molecule (rotation, translation and centre).

The command '`reset world`' restores the world parameters (rotation, translation) and sets the scale to its default value.

The command '`reset worlddepth`' restores the worlddepth parameters to its default value.

The result of the command '`reset`' depends on the active state of the world. If the world is active (see '`rotate all`'), this command is equivalent to '`reset world`', thus protecting the world assembly. If the world is not active (see '`rotate molecule`'), this command is equivalent to '`reset molecule`'.

The command '`reset headlight`' restores the default lighting (see '`set headlight default`' command).

The command '`reset slab`' restores internal slab plane parameters and inactivates slabmode if active. The command '`reset depth`' acts similarly.

The command '`reset bonds`' restores all bond parameters to their initial values, including bond creation, bond deletion, bond rotation, and bond order.

The command '`reset all`' includes the commands '`reset world`', '`reset slab`', '`reset depth`', '`reset headlight`', and '`reset bonds`'.

### `` Restrict

    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 affect 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`' on the command line for more information on RasMol atom expressions or consult the document on atom expressions and the predefined atom sets.

### `` Ribbons

    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 Ångstroms) for nucleic acids. The default width of protein alpha helices and beta sheets is 380 (1.52 Ångstroms) and 100 (0.4 Ångstroms) 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.

### `` Rotate

    Syntax: rotate <axis> {-} <value>
    	rotate bond {<boolean>}
    	rotate molecule {<boolean>}
    	rotate all {<boolean>}

Rotate the molecule about the specified axis. Permitted values for the axis parameter are "`x`", "`y`" and "`z`". The integer parameter states the angle in degrees for the structure to be rotated. For the X and Y axes, positive values move the closest point up and right, and negative values move it down and left, respectively. For the Z axis, a positive rotation acts clockwise and a negative angle anti-clockwise.

Alternatively, this command may be used to specify which rotations the mouse or dials will control. If 'rotate bond true' is selected, the horizontal scroll bar will control rotation around the axis selected by the 'bond src dst pick' command. If 'rotate all true' is selected, and multiple molecules have been loaded, then all molecules will rotate together. In all other cases, the mouse and dials control the the rotation of the molecule selected by the molecule n' command.

RasTop Specific:

    Syntax: rotate <axis> {-} <value>
    	rotate world <axis> {-} <value>
    	rotate bond <value>
    	rotate molecule {<boolean>}
    	rotate all {<boolean>}

The '`rotate <axis>`' command rotates the active molecule. Only one molecule is moved at a time; other loaded molecules and the world origin are not moved. The rotation center is always located in the bounding box of the molecule and changed if necessary. The command is independent of the '`rotate all`' and '`rotate molecule`' state ('off' or 'on').

The '`rotate world <axis>`' command rotates the entire world, even when only one molecule is loaded. If not rotation center is specified, the rotation occurs around the world origin.

The '`rotate bond`' command rotates around the bond axis selected by the 'bond src dst pick' command.

### `` Save

There is no distinction between the '`save`' and the '`write`' command.

    Syntax:  save {world|molecule} {<filename>}

    Syntax:  save  <format> <filename>
                    pdb <filename>
                    mdl <filename>
                    alchemy <filename>
                    xyz <filename>

                    iris
                    ppm
                    ras
                    ps
                    epsf
                    monops
                    pict

                    vectps
                    script
                    molscript
                    kinemage
                    povray
                    vrml

                    phipsi
                    rdf, ramachandrandatafile
                    rpp, ramachandranprinterplot

Saving <*.rsm> scripts:

The '`save <filename>`' command will just do that. If the file has been modified, a simple '`save'` command without specified filename will save the file automatically. By default, all molecules are saved ( '`save world'` option).

Note: Files are modified by virtually all RasMol commands; resizing a screen is an exception.

Saving molecular files:

A format keyword and a filename are required. For example '`save pdb <filename>`' save the currently selected set of atoms in a Protein Data Bank (PDB) format file. Only selected atoms of the currently selected molecule are saved. Accepted formats are: PDB, MDL, Alchemy(tm) and XYZ format. Atom coordinates are saved in the current coordinate system. The format Alchemy in molecular coordinates saves also the current rotation. If the world contains 2 (or more) molecules, two (or more) separate files must be generated and joined manually to create a unique molecular file; make sure you do not save the files in molecular coordinates.

Saving image files:

A format keyword is required. The following formats are supported:

> > '`bmp`' (Microsoft bitmap),
> > '`gif`' (Compuserve GIF),
> > '`iris`' (IRIS RGB),
> > '`ppm`' (Portable Pixmap),
> > '`ras`' (Sun rasterfile),
> > '`ps`' and '`epsf`' (Encapsulated PostScript),
> > '`monops`' (Monochrome Encapsulated PostScript),
> > '`pict`' (Apple PICT),
> > '`vectps`' (Vector Postscript).

As of RasTop 2.1, only the 'bmp' and 'pict' formats are working properly in 32-bits. To save 'gif' file, please use the 8-bits version.

Saving script files:

See above for <*.rsm> scripts; 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 following formats are useful for further processing: '`povray`' (POVRay, version 3.5 ), '`vrml`' (VRML file).

Note: As of RasTop 2.1, only the formats '`script`' and '`povray`' are working properly (although not every details of the scenery are saved in povray). If the molecular coordinates system is used to export POVRay scripts, only the active molecule is saved (in molecular coordinates), otherwise all objects are saved.

Saving data file:

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).

### `` Scale

    Syntax:  scale <value>

The scale command changes the magnification of the currently displayed image. The value determines the distance of the smallest size of the window screen either in RU if it is an integer number or in angstrom if it is a floating number. This command is an alternative to the '`zoom`' command that is independent of the worlddepth parameter.

### `` Script

    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 complicated 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.

Scripts may also be created with a text editor.

    RasTop Specific:

    Syntax:  script default <filename>

This command allows a script to run automatically after any molecular files loaded, thus replacing the standard RasMol initial representation. The file name is saved for future sessions.

### `` Select

    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 affect 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`' on the command line for more information on RasMol atom expressions or consult the document on atom expressions and the predefined atom sets.

RasTop specific:

    Syntax:  select previous

Select the atoms that were selected before the last '`select`' command.

    Syntax: select <</>> x1{-x2},...,xi{-xi+1},...<</>>

This INTERNAL command is used to describe atom sets in rsm scripts generated by RasTop. The character '`<`' or '`>`' immediately following the '`select`' keyword escapes the parser. Each block describes a subset of atoms bearing consecutive numbers that is added to the current selection. Wrong blocks are ignored as well undefined atom numbers. The character '`<`' starts a new selection at the beginning of a line and continues the selection at the end; the character '`>`' continues the selection at the beginning of the line and ends it at the end.

RasTop specific:

    Syntax:  select view

This command selects all atoms present in the current view. This is a scripting alternative to atom selection using the lasso.

### `` Set

    Syntax:  set <parameter> {<option>}

The RasMol '`set`' command allows the user to alter various internal program parameters such as those controlling rendering options. Each parameter has its own set or permissible parameter options. Typically, omitting the parameter option resets that parameter to its default value. A list of valid parameter names is given below.

Ambient | Axes | Background | BackFade | BondMode | Bonds | BoundBox | Cartoon
CisAngle | Coordinates | Display | FontSize | FontStroke | HBonds | Hetero | HourGlass
Hydrogen | Kinemage | Light | Menus | Monitor | Mouse | Picking | Radius
ShadePower | Shadow | SlabMode | Solvent | Specular | SpecPower | Stereo | SSBonds
Strands | Transparent | UnitCell | VectPS | World | Write

### `` Show

    Syntax:  show information
             show phipsi
             show RamPrint
             show selected { group | chain | atom }
             show sequence
             show symmetry

    RasTop Specific:

    	show world
    	show worlddepth

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 phipsi`' shows the phi and psi angles of the currently selected residues and the omega angles of cis peptide bonds. The command '`show RamPrint`' (or 'show RPP' or 'show RamachandranPrinterPlot') shows a simple Ramachandran printer plot in the style of Frances Bernstein's fisipl program. The command '`show selected`' (or 'show selected group' or 'show selected chain' or 'show selected atom' ) shows the groups (default), chains or atoms of the current selection. The command '`show sequence`' lists the residues that comprise each chain of the molecule. The command '`show symmetry`' shows the space group and unit cell of the molecule.

The command '`show world`' lists information regarding world center and world axes position and all loaded molecules with position in world and absolute coordinates. The command '`show worlddepth`' lists the actual and the default worlddepth.

### `` Slab

    Syntax:  slab {<boolean>}
             slab <value>

The RasMol '`slab`' command enables, disables or positions the z-clipping plane of the molecule. The program only draws those portions of the molecule that are further from the viewer than the slabbing plane. Integer values range from zero at the very back of the molecule to 100 which is completely in front of the molecule. Intermediate values determine the percentage of the molecule to be drawn.

This command interacts with the '`depth`' command, which clips to the rear of a given z-clipping plane.

RasTop Specific:

    Syntax:  slab world origin
             slab world <value>

The '`slab world origin`' command sends the clipping plane at the world origin. The '`slab world <value>`' command moves the plane of value Angstroms (if value if a floating number) or value RasMol units (if value is an integer) relatively to its current position. Future versions of RasMol may not adopt this convention.

### `` Spacefill

    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, '`spacefill 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 Ångstrom) or a value containing a decimal point. A value of 500 (2.0 Ångstroms) or greater results in a "Parameter value too large" error. A negative value indicates a percentage of van des Waals radius.

The '`temperature`' option sets the radius of each sphere to the value stored in its temperature field. Zero or negative values have no effect and values greater than 2.0 are truncated to 2.0. The '`user`' option allows the radius of each sphere to be specified by additional lines in the molecule's PDB file using Raster 3D's COLOUR record extension.

The RasMol command '`cpk`' is synonymous with the '`spacefill`' command.

### `` SSBonds

    Syntax:  ssbonds {<boolean>}
             ssbonds <value>

The RasMol '`ssbonds`' command is used to represent the disulphide bridges of the protein molecule as either dotted lines or cylinders between the connected cysteines. The first time that the '`ssbonds`' command is used, the program searches the structure of the protein to find half-cysteine pairs (cysteines whose sulphurs are within 3 Ångstroms 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.

### `` Star

    Syntax:  star {<boolean>}
             star temperature
             star user
             star <value>

The RasMol '`star`' command is used to represent all of the currently selected atoms as stars (six strokes, one each in the x, -x, y, -y, z and -z directions). The commands '`select not bonded`' followed by '`star 75`' are useful to mark unbonded atoms in a '`wireframe`' display with less overhead than provided by '`spacefill 75`'. This can be done automatically for all subsequent wireframe displays with the command '`set bondmode not bonded`'.

The command '`star true`', the default, represents each atom as a star with strokes length equal to van der Waals radius. The command '`star off`' turns off the representation of the selected atom as stars. A star stroke length may be specified as an integer in RasMol units (1/250th Ångstrom) or a value containing a decimal point. A value of 500 (2.0 Ångstroms) or greater results in a "Parameter value too large" error.

The '`temperature`' option sets the stroke length of each star to the value stored in its temperature field. Zero or negative values have no effect and values greater than 2.0 are truncated to 2.0. The '`user`' option allows the stroke length of each star to be specified by additional lines in the molecule's PDB file using Raster 3D's COLOUR record extension.

The RasMol '`spacefill`' command can be used for more artistic rendering of atoms as spheres.

RasTop specific:
Spheres and stars are mutually exclusive, i.e. only one of the two representations is used at a time for a given atom.

### `` Stereo

    Syntax:  stereo on
             stereo [-]<number>
             stereo off

The RasMol '`stereo`' command provides side-by-side stereo display of images. Stereo viewing of a molecule may be turned on (and off) either by selecting '`Stereo`' from the '`Options`' menu, or by typing the commands '`stereo on`' or '`stereo off`'. The separation angle between the two views may be adjusted with the '`set stereo [-] <number>`' command, where positive values result in crossed eye viewing and negative values in relaxed (wall-eyed) viewing. The inclusion of '`[-] <number>`' in the '`stereo`' command, as for example in '`stereo 3`' or '`stereo -5`', also controls angle and direction.

The stereo command is only partially implemented. When stereo is turned on, the image is not properly recentred. (This can be done with a '`translate x -<number>`' command.) It is not supported in vector PostScript output files, is not saved by the '`write script`' command, and in general is not yet properly interfaced with several other features of the program.

### `` Strands

    Syntax:  strands {<boolean>}
             strands <value>
             strands dash

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 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 Ångstroms wide). The default width of protein alpha helices and beta sheets is 380 (1.52 Ångstroms) and 100 (0.4 Ångstroms) 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.

### `` Structure

    Syntax:  structure

The RasMol '`structure`' command calculates secondary structure assignments for the currently loaded protein. If the original PDB file contained structural assignment records (HELIX, SHEET and TURN) these are discarded. Initially, the hydrogen bonds of the current molecule are found, if this hasn't been done already. The secondary structure is then determined using Kabsch and Sander's DSSP algorithm. Once finished the program reports the number of helices, strands and turns found.

### `` Trace

    Syntax:  trace {<boolean>}
             trace
             trace temperature
             trace dots <value>

The RasMol '`trace`' command displays a smooth spline between consecutive alpha carbon positions. This spline does not pass exactly through the alpha carbon position of each residue, but follows the same path as '`ribbons`', '`strands`' and '`cartoons`'. Note that residues may be displayed as '`ribbons`', '`strands`', '`cartoons`' or as a '`trace`'. Enabling one of these representations disables the others. However, a residue may be displayed simultaneously as backbone and as one of the above representations. This may change in future versions of RasMol. Prior to version 2.6, '`trace`' was synonymous with '`backbone`'.

'`Trace temperature`' displays the backbone as a wider cylinder at high temperature factors and thinner at lower. This representation is useful to X-ray crystallographers and NMR spectroscopists.

'`Trace dots`' displays the backbone as a series of dots. This commands is useful to link parts of the molecule represented with a full cylinder. The subcommand '`<value>`' is RasTop specific and fixe the radius of the dots.

### `` Translate

    Syntax:  translate <axis> {-} <value>

The RasMol '`translate`' command moves the position of the centre of the molecule on the screen. The axis parameter specifies along which axis the molecule is to be moved and the integer parameter specifies the absolute position of the molecule centre from the middle of the screen. Permitted values for the axis parameter are "`x`", "`y`" and "`z`". Displacement values must be between -100 and 100 which correspond to moving the current molecule just off the screen. A positive "`x`" displacement moves the molecule to the right, and a positive "`y`" displacement moves the molecule down the screen. The pair of commands '`translate x 0`' and '`translate y 0`' centers the molecule on the screen.

RasTop Specific:

The displacement values in the classical RasMol command are expressed in percent of either the screen width or the screen height; displacement values along the Z-axis are ineffective. In RasTop, the 3 axis are active. Displacements values are expressed in percent of the smallest screen side, either width or height. Translation displacements are limited in RasMol to values between -100 and 100. In RasTop, displacement are unlimited. See also the command '`position`' , which places molecules independently of the zoom value.

    Syntax:  translate world <axis> {-} <value>

The '`translate world`' command translates the origin of the world and all molecules along the X- and the Y-axis. Displacement values along the Z-axis are made relatively to the world plane.

### `` UnBond

    Syntax: unbond <number> <number>

The RasMol command 'unbond <number> <number>' removes the designated bond from the drawing.
The command 'unbond' without arguments removes a bond previously picked by the 'bond <number> <number> pick' command.

### `` Wireframe

    Syntax:  wireframe {<boolean>}
             wireframe <value>
             wireframe dash

The RasMol 'wireframe' command represents each bond within the selected region of the molecule as a cylinder, a line, a dashed line, or a 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 Ångstroms. A parameter value of 500 (2.0 Ångstroms) or above results in an "Parameter value too large" error. Bonds may be coloured using the 'colour bonds' command.

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.

### `` Write

The distinction between this command and the RasMol '`save`' command has been dropped; See RasMol '`save`' command.

### `` Zap

    Syntax:  zap {all | world }
    	zap selected
    	zap molecule

    RasTop Specific:

Deletes the contents of all current databases and resets parameter variables to their initial default state. The command '`zap selected`' or '`zap molecule`' deletes only the active molecule.

### `` Zoom

    Syntax:  zoom {<boolean>}
             zoom <value>

Change the magnification of the currently displayed image. Boolean parameters either magnify or reset the scale of current molecule. An integer parameter 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.

RasTop specific:

    Syntax:  zoom world <value>

Change the magnification of the currently displayed image from the center of the screen, independently of the actual center position, giving a zoom-translation effect.

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