Script Reference
These methods and properties are provided in order to conform to embedded molecules which use scripting. Most of them are not implemented, and are here merely to prevent breakage of existing scripts. They may be implemented in the future if this is requested.
The methods and properties described below are provided to give backward compatability to RasMol and various other programs whose APIs conform to this model. However, no source code from any of these programs was used to provide these functions.
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- on|off
- 1|0
- 1.0|0.0
- true|false
- yes|no
- all|none
- Note: case insensitive
Takes a value and interprets it as either true or false. Any value which does not match the above syntax is taken to be true.
Many of the functions take a boolean parameter value. They are flexible in that any of the above alternates will work.
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- aliceblue|antiquewhite|...|yellow|yellowgreen
- RRGGBB
- Note: case insensitive
Takes the name or hex value of a colour. The complete list of colour names can be found here: W3C SVG Colour Keywords Hex values are 00 - FF for each of red, green and blue.
Many of the functions take a colour value. They are flexible in that any of the above alternates will work.
- background green
- fgcolor black
- set background pink
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Takes a value and interprets it as a floating point value.
Floating point numerical value.
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Takes a value and interprets it as an integer value.
A whole number, positive or negative.
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Takes a value and interprets it as a positive integral value.
A whole positive number.
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- about
- [Right Click Menu]->About
Displays the "About" information
Displays the "About" information such as product name, contact information and version number in a seperate browser tab.
- [Right Click Menu]->About includes a call toabout
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- animboolean
- anim info
- anim mode { loop | once | palindrome }
- anim direction {+1|-1}
- anim fpspositive-integer
- anim frame {next|-1|positive-integer}
- [Right Click Menu]->Animate->Stop
- [Right Click Menu]->Animate->Loop
- [Right Click Menu]->Animate->Palindrome
Sets the animation mode, direction and speed. You can use either anim or animation as the command
You must specify one of the following settings. There is no default setting.
on - starts playing the animation
off - stops the animation
info - shows animation information (you can also use show animation)
mode - sets how the animation starts and ends. If you use anim mode, you must specify one of the following settings:
-loop - loop from start to end and repeat -once - loop from start to end once -palindrome - loop start to end, then end to start, and repeat
direction - sets the current play direction. If you use anim direction, you must specify one of the following settings:
- +1 - advances to the next animation frame in the current direction
- -1 - moves to the previous frame
fps - frames per second. If you use anim fps, you must specify: positive-integer - number of frames per second
frame - sets which frame to be displayed. If you use anim frame, you must specify one of the following settings:
- next - advances to the next animation frame in the current direction
- -1 - moves to the previous frame
- positive-integer - jumps to the specified frame number
- [Right Click Menu]->Animate->Stop includes a call toanim false
- [Right Click Menu]->Animate->Loop includes a call toanim mode LOOP
- [Right Click Menu]->Animate->Palindrome includes a call toanim mode PALINDROME____________________________________________________________
alias anim
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alias atoms ____________________________________________________________
- atomsboolean
- [Right Click Menu]->Style->Atoms
Display atoms, as opposed to residues .
- [Right Click Menu]->Style->Atoms includes a call toatoms true
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- attitudeboolean
- [Right Click Menu]->Overlay->Attitude Indicator
Display the attitude instrument overlay.
- [Right Click Menu]->Overlay->Attitude Indicator toggles a call toattitude true|false
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- backboneboolean
- backbonefloat
- backbone dash
- [Right Click Menu]->Style->Backbone Off
- [Right Click Menu]->Style->Backbone Tube
Show the backbone chain which joins the residues in a poly-residue molecule.
- [Right Click Menu]->Style->Backbone Off includes a call tobackbone false
- [Right Click Menu]->Style->Backbone Tube includes a call tobackbone true
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alias bgcolour ____________________________________________________________
alias bgcolour ____________________________________________________________
alias bgcolour
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Create a bond
The command 'bond positive-integer positive-integer +' adds a new bond between the specified atoms, or increases the bond order if such a bond already exists. The 'pick' command chooses the centre of rotaion for the rotate bond command.
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Display a molecule's ribbons as Richardson (MolScript) style protein 'cartoons'.
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alias cartoon
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alias centre ____________________________________________________________
- centre {<expression>} {translate|center}
- center {<expression>} {translate|center}
Define the point about which the molecule rotates.
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alias centreat ____________________________________________________________
alias centreat ____________________________________________________________
alias centreat ____________________________________________________________
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Place a copy of the currently displayed image on the local graphics clipboard.
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alias colour ____________________________________________________________
- 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.
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Recalculate the connectivity of the current molecule.
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alias spacefill ____________________________________________________________
alias spacefill
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- define <identifier> <expression>
Associate an arbitrary set of atoms with a unique identifier
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alias pause
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Enable, disable or position the back-clipping plane of the molecule.
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alias display
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Generate a van der Waals' dot surface around the currently selected atoms.
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Display a message.
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Sets the menus and messages to the English versions.
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alias English
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Exit a script.
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alias fgcolour ____________________________________________________________
alias fgcolour
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Sets the menus and messages to the French versions.
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alias French
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alias geosurface ____________________________________________________________
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alias getproperty ____________________________________________________________
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Represent the hydrogen bonding of the protein molecule's backbone.
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- help {<topic> {<subtopic>}}
- ? {<topic> {<subtopic>}}
- [Right Click Menu]->Help
On-line help on the given topic.
- [Right Click Menu]->Help includes a call tohelp
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Allows molecualr data to be embedded directly into the web page.
Note that special precautions need to be taken with white-space, as it is not preserved by HTML. For example, all newlines should be coded as &xA; An optional <EOF> can be placed at the end of the string, to preserve trailing white-space which would otherwise be lost.
<object type="chemical/x-xyz" width="640" height="480" > <param name="inline" value="3&xA; Water&xA; O 4.013 0.831 -9.083&xA; H 4.941 0.844 -8.837&xA; H 3.750 -0.068 -9.293&xA; "/> </object> ____________________________________________________________
alias pause
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alias invertsel ____________________________________________________________
alias invertsel ____________________________________________________________
alias invertsel ____________________________________________________________
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Sets the menus and messages to the Italian versions.
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alias Italian
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- label {<string>}
- label <boolean>
- [Right Click Menu]->Style->No Labels
- [Right Click Menu]->Style->Symbols
- [Right Click Menu]->Style->Name Labels
Allows an arbitrary formatted text string to be associated with each currently selected atom.
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 M NMR Model Number (with leading "/") A Alternate Conformation Identifier (with leading ";")
- [Right Click Menu]->Style->No Labels includes a call tolabel false
- [Right Click Menu]->Style->Symbols includes a call tolabel e
- [Right Click Menu]->Style->Name Labels includes a call tolabel a____________________________________________________________
alias label
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alias lcaocartoon ____________________________________________________________
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- legendboolean
- [Right Click Menu]->Overlay->Legend
- [Right Click Menu]->Overlay->Legend toggles a call tolegend true|false
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- load {<format>} <filename>
Load a molecule coordinate file
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alias inline ____________________________________________________________
alias inline
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alias monitor
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alias frame
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Selects one of the previously loaded molecules for active manipulation.
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alias monitor ____________________________________________________________
alias monitor
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alias moveto ____________________________________________________________
- moveto timeSeconds FRONT|BACK|LEFT|RIGHT|TOP|BOTTOM
- moveto timeSeconds {x y z} degrees zoomPercent transX transY {x y z} rotationRadius navigationCenter navTransX navTransY navDepth
- [Right Click Menu]->Navigate->Front
- [Right Click Menu]->Navigate->Back
- [Right Click Menu]->Navigate->Left
- [Right Click Menu]->Navigate->Right
- [Right Click Menu]->Navigate->Above
- [Right Click Menu]->Navigate->Below
The moveto command rotates the molecule to a predefined orientation.
Two formats can be used. In each, the first (optional) parameter specifies the number of seconds during which the molecule should rotate smoothly from the current orientation to the new orientation. A 0 for this first parameter specifies an instantaneous reorientation. In conjunction with "show orientation" this command allows reading and restoring specific user-specified orientations.
moveto timeSeconds FRONT|BACK|LEFT|RIGHT|TOP|BOTTOM
A simple use of moveTo just has six optional directions.
moveto timeSeconds {x y z} degrees zoomPercent transX transY {x y z} rotationRadius navigationCenter navTransX navTransY navDepth
In the second option, the second parameter is a coordinate {x, y, z} defining the axis relative to the default orientation about which the molecule should be rotated. The third parameter is the counterclockwise (right-hand) rotation in degrees about this axis. "moveto 0 {0 0 0} 0" rotates the model to the default orientation (equivalent to "reset"). If the angle parameter is 0 but any one of x, y, or z is nonzero, then no reorientation occurs (because the axis has been specified, but the rotation is 0 degrees). Following these parameters is the zoom setting in percent, the X- and Y-positions of the rotation center on the screen, as percent of width and height, respectively. The actual molecular coordinate of the rotation center along with the rotation radius (which determines the magnification associated with ZOOM 100) are next. The final parameters define the navigation center molecular coordinate, its X- and Y- position on the screen in percent, and the depth of the navigation point in percent of model depth (100 = front, 0 = rear). In conjunction with "show/save/restore orientation" this command allows reading and restoring specific user-specified orientations.
moveto timeSeconds {x y z} degrees 0 transX transY (atom expression) 0 zoomAdjustment navigationCenter navTransX navTransY navDepth
If the zoom setting prior to translation positions is 0, and an atom expression is used for the point, then the moveTo can be designed to automatically zoom to the scale that would fill the screen with that set of atoms. The optional zoom adjustment is in the form +n, -n, n, or /n, as for zoomTo.
moveto timeSeconds {x y z} degrees (atom expression) 0 zoomAdjustment navigationCenter navTransX navTransY navDepth
If no translation is involved, then there is also no need for the zoom setting of 0 prior to the atom expression.
Examples: in new window using 1crn.pdb moveto 0 1 0 0 -90; view from top moveto 0 0 1 0 90; view from right moveto 0 0 1 0 -90; view from left moveto 2 1 0 0 90; view from bottom with smooth 2-second transition moveto 0 0 0 0 0 200; default orientation with instantaneous transition and a zoom of 200%
- [Right Click Menu]->Navigate->Front includes a call tomoveto 1 front
- [Right Click Menu]->Navigate->Back includes a call tomoveto 1 back
- [Right Click Menu]->Navigate->Left includes a call tomoveto 1 left
- [Right Click Menu]->Navigate->Right includes a call tomoveto 1 right
- [Right Click Menu]->Navigate->Above includes a call tomoveto 1 top
- [Right Click Menu]->Navigate->Below includes a call tomoveto 1 bottom
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- navigate {walk|fly|examine|lookat|examine_zoom}
- [Right Click Menu]->Navigate->Examine Mode
- [Right Click Menu]->Navigate->Zoom Mode
- [Right Click Menu]->Navigate->Examine Mode includes a call tonavigate examine
- [Right Click Menu]->Navigate->Zoom Mode includes a call tonavigate examine_zoom
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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.
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- polargridboolean
- [Right Click Menu]->Overlay->Polar Grid
- [Right Click Menu]->Overlay->Polar Grid toggles a call topolargrid true|false
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Print the currently displayed image
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alias exit
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Redraws the current image.
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Sequentially numbers the residues in a macromolecular chain.
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Restores the original viewing transformation and centre of rotation.
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- residuesboolean
- [Right Click Menu]->Style->Residues
- [Right Click Menu]->Style->Residues includes a call toresidues true
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Defines the currently selected region of the molecule.
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- reticuleboolean
- [Right Click Menu]->Overlay->Reticule
- [Right Click Menu]->Overlay->Reticule toggles a call toreticule true|false____________________________________________________________
alias reticule
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alias ribbons ____________________________________________________________
- ribbonsboolean
- ribbonsfloat
- [Right Click Menu]->Style->Backbone Off
- [Right Click Menu]->Style->Backbone Ribbon
Displays the currently loaded protein or nucleic acid as a smooth solid "ribbon" surface passing along the backbone of the protein.
- [Right Click Menu]->Style->Backbone Off includes a call toribbons false
- [Right Click Menu]->Style->Backbone Ribbon includes a call toribbons true
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alias rocket
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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 mouseand dials control the the rotation of the molecule selected by the 'molecule n' command.
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alias rotatesel ____________________________________________________________
alias rotatesel ____________________________________________________________
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alias rotatesel
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- rulerboolean
- [Right Click Menu]->Overlay->Ruler
- [Right Click Menu]->Overlay->Ruler toggles a call toruler true|false
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- save {pdb} <filename>
- save mdl <filename>
- save alchemy <filename>
- save xyz <filename>
Save the currently selected set of atoms in a CML format file.
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Reads a set of commands sequentially and executes them.
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Define the currently selected region of the molecule.
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alias selhalos ____________________________________________________________
alias selhalos ____________________________________________________________
alias selhalos ____________________________________________________________
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- set <parameter> {<option>}
Set one of the properties
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- show information
- show centre
- show phipsi
- show RamPrint
- show rotation
- show selected { group | chain | atom }
- show sequence
- show symmetry
- show translation
- show zoom
Display details of the status of the currently loaded molecule.
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- skygroundboolean
- [Right Click Menu]->Overlay->Sky/Ground
- [Right Click Menu]->Overlay->Sky/Ground toggles a call toskyground true|false
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Enables, disables or positions the z-clipping plane of the molecule.
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alias script
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- spacefillboolean
- spacefill temperature
- spacefill user
- spacefillfloat
- [Right Click Menu]->Style->Ball and Stick
- [Right Click Menu]->Style->Space Filling
- [Right Click Menu]->Style->Formula
Represent all of the currently selected atoms as solid spheres.
- [Right Click Menu]->Style->Ball and Stick includes a call tospacefill 0.3
- [Right Click Menu]->Style->Space Filling includes a call tospacefill true
- [Right Click Menu]->Style->Formula includes a call tospacefill false
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Sets the menus and messages to the Spanish versions.
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alias Spanish
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- spinboolean
- [Right Click Menu]->Animate->Spin
- [Right Click Menu]->Animate->Spin includes a call to togglespin true|false____________________________________________________________
alias inline ____________________________________________________________
alias inline
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alias ssbonds
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Represent all of the currently selected atoms as stars (six strokes, one each in the x, -x, y, -y, z and -z directions).
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alias spin
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Provides side-by-side stereo display of images.
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alias strands
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Calculates secondary structure assignments for the currently loaded protein
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Renders a Lee-Richards molecular surface resulting from rolling a probe atom on the selected atoms.
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Displays a smooth spline between consecutive alpha carbon positions.
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- translate <axis> {-}float
Moves the position of the centre of the molecule on the screen.
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alias transsel ____________________________________________________________
alias transsel ____________________________________________________________
alias transsel ____________________________________________________________
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Remove a bond
Removes the designated bond from the drawing.
The command 'unbond' without arguments removes a bond previously picked by the 'bond positive-integer positive-integer pick' command.
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alias unitcell ____________________________________________________________
alias resume
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alias vector
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- viewsrc
- [Right Click Menu]->View CML Source
- [Right Click Menu]->View CML Source includes a call toviewsrc____________________________________________________________
alias pause
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- wireframeboolean
- wireframefloat{}
- [Right Click Menu]->Style->Ball and Stick
- [Right Click Menu]->Style->Space Filling
- [Right Click Menu]->Style->Formula
Represents each bond within the selected region of the molecule as a cylinder, a line or a depth-cued vector.
- [Right Click Menu]->Style->Ball and Stick includes a call towireframe 0.1
- [Right Click Menu]->Style->Space Filling includes a call towireframe 0.1
- [Right Click Menu]->Style->Formula includes a call towireframe false
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- write {<format>} <filename>
Write the current image to a file in a standard format.
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- xygridboolean
- [Right Click Menu]->Overlay->xy Grid
- [Right Click Menu]->Overlay->xy Grid toggles a call toxygrid true|false
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- xzgridboolean
- [Right Click Menu]->Overlay->xz Grid
- [Right Click Menu]->Overlay->xz Grid toggles a call toxzgrid true|false
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- yzgridboolean
- [Right Click Menu]->Overlay->yz Grid
- [Right Click Menu]->Overlay->yz Grid toggles a call toyzgrid true|false
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Deletes the contents of the current database and resets parameter variables to their initial default state.
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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.
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alias zoomto ____________________________________________________________
- zoomtotimeSeconds percentZoom
- [Right Click Menu]->Navigate->Zoom In
- [Right Click Menu]->Navigate->Zoom Out where [time-in-seconds] is in (seconds) [percent-zoom] is an (integer, 5 to 200000)
Carries out a smooth transition to the specified zoom setting. Indicating a new rotation center is optional.
zoomto
By itself, zoomTo smoothly zooms IN by a factor of 2 over the course of 1 second.
zoomto OUT
Smoothly zooms OUT by a factor of 2 over the course of 1 second.
zoomto [time-in-seconds] (atom expression) or {x y z}
Smoothly moves the specified atom or coordinate to the center of the window if windowCentered or designates it as the center of rotation if not windowCentered. If the atom is already the rotation center, then this command zooms in on the atom by a factor of two. All parameters are options. The default time is 1 second; indicating no center position results in simple, smooth zooming; indicating no zoom defaults to twice the current zoom setting.
zoomto [time-in-seconds] (atom expression) or {x y z} [percent-zoom]
Smoothly transitions to the indicated zoom setting over the course of the specified number of seconds.
zoomto [time-in-seconds] (atom expression) or {x y z} + or - delta
Adds or subtracts an absolute amount from the current zoom setting over the course of the specified number of seconds.
zoomto [time-in-seconds] (atom expression) or {x y z} * or / factor
Multiplies or divides the current zoom setting by the indicated factor over the course of the specified number of seconds.
zoomto [time-in-seconds] (atom expression) or {x y z} 0
Zooms to the setting that fills the screen with the designated atoms. (Requires set perspectiveModel 11 for proper operation.) Can include modifiers +n, -n, *n, /n after the 0.
- [Right Click Menu]->Navigate->Zoom In includes a call tozoomto
- [Right Click Menu]->Navigate->Zoom Out includes a call tozoomto OUT
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The amount of ambient light in a scene, between 0 and 100 per cent intensity of the darkest shade.
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alias spinfps ____________________________________________________________
- animmode { loop | once | palindrome }
Sets the animation mode
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Show or hide orthogonal co-ordinate axes.
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Fade to the background colour, rather than black.
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alias bgcolour ____________________________________________________________
alias bgcolour ____________________________________________________________
alias bgcolour ____________________________________________________________
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.
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alias bgcolour
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- bondmode [and | or | all | none | not bonded]
Determines how bonds are selected.
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Show or hide bounding box of molecule
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Set the caption text, written at the top of the window..
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Show or hide the cartoon version of the "ribbons" display. The number sets the cartoon depth.
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alias cartoon
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Set atomic charge on selected atoms.
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Cutoff angle for identifying cis peptide bonds, defaults to 90 degrees.
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Set the blending colour.
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Enable or disable subsequent delay commands in a script.
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- display [ selected | normal ]
Switch highlighting of selected portions of the molecule.
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Display in a two dimensional rendering.
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- display3d { backbone | ball&stick | cartoons | ribbons | spacefill | sticks | strands | wireframe }
Switch the 3D rendering mode.
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alias fgcolour ____________________________________________________________
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Set the pixel height of label characters. FS or PS are fixed or proportional spacing.
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Size of stroke width.
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Contour level used when reading gaussian files, in Angstroms, default 0.2
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alias groundcolour ____________________________________________________________
Set the colour depicting ground in the sky-ground background. Default is green.
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- hbonds [ backbone | sidechain ]
Draw hydrogen bonds either between donor/acceptor, or between the backbone atoms of a protein or nucleic acid.
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Switch whether selections include heterogenous atoms.
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Enable or disable the use of the "busy" cursor.
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Whether or not selections include hydrogens.
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Amount of detail in a written kinemage file.
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Set whether the same molecule can be re-loaded.
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alias menus ____________________________________________________________
Enable the menu buttons, or bar.
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- mep [ mode | distance | function ]float
Various settings for MEP texture mapping
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- mlp [ mode | distance | function ]float
Various settings for MLP texture mapping
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The MIME type of the molecular data.
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Allows the display of distance monitors, which are dashed lines between atom pairs.
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alias monitor
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- mouse [ rasmol | insight | quanta ]
Sets the navigation characteristics of mouse movement.
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Switches on or off animation of subsequent moves.
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How molecules are interacted with on the screen.
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Sets the radius of the probe sphere ( solvent ) used to calculate the "dots" solvent accessibility surface. An integer value is in rasmol units, a float value is in Angstroms.
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A percentage between 0 and 100 governing how shiny objects appear.
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Enables or disables ray-tracing.
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alias skycolour ____________________________________________________________
Sets the sky colour in the sky-ground background. Default blue.
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- slabmode [reject | half | hollow | solid | section]
Controls how objects appear if they are cut by the z-clipping plane ( i.e. objects that are partially too near or too far to be seen ).
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Switches the "dots" function between van der Waals and solvent accessible surface.
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Between 0 and 100 adjust the strength of specular highlighting.
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Enable or disable specular highlights on solid objects.
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Turn on or off spinning.
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Set spin frames per second.
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Set the speed of spinning around the x-axis, in degrees per second.
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Set the speed of spinning around the y-axis, in degrees per second.
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Set the speed of spinning around the z-axis, in degrees per second.
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- ssbondsboolean
- ssbonds [backbone | sidechain]
Controls how sulphur-sulphur bonds are calculated and displayed.
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Controls viewing of side-by-side stereo images. The float value is the seperation angle between the two views. Positive angles are cross-eyed, negative are wall-eyed.
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Number of strands in a ribbon.
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alias caption
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Controls whether subsequent write gif commands produce transparent backgrounds.
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Switch on or off the display of the crystallographic unit cell.
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Enable or disable black outlining in postscript output files.
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Allow or deny file writing from within scripts.
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alias zoom_centre ____________________________________________________________
Translate the centre of rotation to the centre of the screen.
