The HTML developer inserts a Chime / Chime Pro plug-in into an HTML page via an EMBED tag (see the Chime / Chime Pro FAQ for an example.) The following options are used to control the embedded Chime / Chime Pro plug-in:
Alphabetical Listing
Listing by Category
Specifies alternate RasMol commands to execute when a button goes from a
"pushed" state to an "unpushed" state. Multiple commands can be separated
with "|" or ";". This tag applies only to toggle or radio buttons, as
specified in the button tag.
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Specifies the animation events (frames) per second.
Note: The value specified
for animfps may not be possible on the viewer's platform. Chime will get
as close as the system allows.
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Specifies the name of a JavaScript function in the current document that is to be called before each event ("frame") of an animation (.xyz) file is displayed. The function should conform to the prototype:
function JSFunctionName( pluginName, frameNumber )
Where pluginName is the value specified in the name
parameter for the Chime structure window in which the animation is playing and
frameNumber is an integer indicating which number event in the
file is about to be displayed.
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Specifies how the the animation is to be presented.
loop - Play the animation from the first frame to the last and then start
again from the first.
once - Play the animation from the first frame to the last and then stop.
palindrome - Play the animation from the first frame to the last and then
backwards from last to first, continuously.
ping - Synonym for palindrome.
pong - Synonym for palindrome.
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Specifies whether to display atom numbers.
on - display atom numbers
off - do not display atom numbers.
Sets the background color for either 2d or 3d rendering.
black - make the background black
white - make the background white
#rrggbb - set the background to a specific color
using an HTML-style color value. For example: #777777 gives a dark gray.
Specifies the standard bond length, in decipoints, used to display a 2D image when using
the tag bondscaling=stdbond. The default length is 180.
Specifies the type of scaling to use when displaying a 2D image.
asdrawn - display the image exactly as it was drawn,
with the same bond lengths and coordinates.
asdrawn_fitbox - display the image with the same
relative bond lengths as were drawn, but scale the whole image to best
fit the Chime structure window.
fitbox - display the image to best fit the Chime
structure window, and make all bonds equal in length.
stdbond - set all bond lengths to the standard bond
length. The standard bond length is specified by the bondlen
tag.
Displays the Chime plug-in as a button. Three types of buttons are available: push, radio and toggle.
When the user clicks a button, the script attached to the button
through the script or csml tag executes.
The script acts on the Chime plug-in indicated by the target tag. A
Chime button can also trigger a JavaScript routine through the
ButtonCallback tag.
In the case of toggle and radio buttons, a second script can be activated
when the button goes from a "pushed" to an "unpushed" state. This script is
specified by the altscript tag.
Because a Chime button does not display a file, you must specify the
mime type manually using the type tag:
type="application/x-spt", as shown in the example.
push - a simple push-button.
radio# - a member of a radio group. Only one member
of the group is pushed at any given time. The group is identified
by the number attached to the tag, for example "radio1", "radio2".
toggle - a toggle button which alternates between a
"pushed" state and an "unpushed" state, similar to a check box.
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Used to specify that a button's initial state is "pushed". If this tag is not used, the button's initial state will be "unpushed".
This tag is only to be used in a Chime button (button=true).
It specifies a JavaScript function in the current document that is to
be called whenever the button is pushed. The function is called twice, once
before execution of the attached RasMol or CSML script, and a second time
afterwards. If there is no attached script, the function is still called
twice.
The JavaScript function must conform to the prototype:
function JSFunctionName( pluginName, executedYet? )
...where pluginName is the name
of the Chime button which the user has pressed, and the boolean
executedYet? is false when
JsFunctionName is first called (before execution of the script)
and true the second time.
With Chime 2.0's new LiveConnect interface, you can start RasMol
scripts from a JavaScript routine when running in Netcape Navigator,
as shown in the example below. In other browsers, you can achieve the
same result by writing a new button with the immediate
tag.
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Specifies the foreground color for a 2D rendering.
black - make the foreground black
sketch - when displaying a sketch file, use the colors specified
in the sketch instead of overriding with a standard color
white - make the foreground white
#rrggbb - set the foreground to a specific color
using an HTML-style color value. For example: #777777 gives a dark gray.
Specifies the color scheme for 3D display.
Specifies any valid CSML script commands to apply to the plug-in. Multiple commands can be separated with a "|" or ";"
When attached to a Chime structure window, the script executes immediately
when the plug-in loads. When attached to a Chime button (button=true),
the script executes in the Chime structure window indicated by the
target tag when the button is pushed.
When debugscript = true, each
line of an executing RasMol script is echoed to the browser's status
line.
false or no - do not echo script commands
true or yes - echo script commands to status line
Forces a 2D rendering of a molecule that would be rendered in 3D by default. Any molecule with 3D coordinates is automatically rendered in 3D unless this tag is used.
Specifies the type of 3D display.
Sets the font used to display atom symbols and other text in 2D display. The default in Windows is Ariel.
Sets the font size, in decipoints, used to display atom symbols and other text in 2D display. The default size is 120.
When frank = true, the "MDL" trademark
is displayed in the lower right corner of the Chime structure window.
Specifies whether, and how, to display hydrogen bonds.
off - do not display hydrogen bonds
on - display hydrogen bonds as dashed lines
number - display hydrogen bonds as cylinders
whose diameter is proportional to the number. See example below.
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Specifies how to display implicit hydrogens in a 2D structure.
asdrawn - display hydrogens as originally drawn.
false - display no implicit hydrogens.
hetero - display implicit hydrogens only on hereoatoms.
terminalhetero - display implicit hydrogens only on terminal
and hetero atoms.
true - display implicit hydrogens on all atoms.
Specifies whether the script attached to a Chime button should be run automatically when the Chime is loaded. This feature allows JavaScript to communicate with Chime by writing a Chime button (to an unseen part of the screen) that will execute immediately to perform some operation on a Chime structure window.
NOTE: Chime 2.0 supports a LiveConnect interface in Netscape Navigator,
providing an easier way to run RasMol scripts from JavaScript. See button
for an example.
false or no - do not run script immediately. Script will
run only when button is pushed.
true or yes - run script immediately upon loading Chime.
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Specifies a JavaScript function in the document that is to be called whenever an informational message is generated by Chime's 3D rendering processes. The function should conform to the prototype:
where pluginName is the name specified
for the Chime structure window and messageText is the
informational message from Chime. Note that if you are using frames you should explicitly
specify the document containing the function, i.e., specify:
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If true, messages generated by normal operation of Chime's
3D rendering engine are echoed to the browser's status line.
false or no - do not echo messages
true or yes - echo messages to status line
Specifies the name of the plug-in. This is needed to make a Chime the
target of a Chime button. It is also used in JavaScript
when executing a script through Chime 2.0's LiveConnect interface. Both techniques
are shown in the example below.
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Sets the MIME type to the NMR pdb mime type so that "multi-frame" pdb files can be loaded.
Specifies 3D display options. If more than one options3d option is specified for the EMBED tag the options will be combined.
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"Foreground" allows Chime to use the colors it needs outside of the current color palette to smoothly display spacefilling structures. This corresponds to the "Force Palette" command on the Chime menu.
Specifies the name of a JavaScript function in the current document that is
to be called whenever a pause command is encountered in a RasMol
script. The function is called twice: once when the pause is
first encountered and again when the script resumes. The function must conform
to the prototype:
function JSFunctionName( pluginName, begPause? )
...where pluginName is the name
of the Chime in which the script is running, and the boolean begPause?
is true when the pause is first encountered and
false when execution of the script resumes.
Specifies the name of a JavaScript function in the current document that is to be called whenever the user clicks on an atom in a Chime structure window. The function should conform to the prototype
function JSFunctionName( pluginName, atomExpression )
...where pluginName is the name
of the Chime structure window and atomExpression
is a string representing the atom (including residue information for a pdb
file) on which the user has clicked.
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Specifies a RasMol script to be executed immediately when the plugin is
loaded, before any file is loaded from the src
tag. Multiple commands can be separated with a "|" or ";".
Specifies a scaling value (in Angstroms per inch) to be used when a 3D
structure is displayed. When the same scale3d value is
used for multiple Chime structure windows on a page, the viewer can get a feel
for the relative size of the structures, as shown in the example.
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Specifies any valid RasMol script commands to apply to the plug-in. Multiple commands can be separated with a "|" or ";".
When attached to a Chime structure window, the script executes immediately
when the plug-in loads. When attached to a Chime button (button=true),
the script executes in the Chime structure window indicated by the
target tag when the button is pushed.
Specifies the frame rate per second for spinning. The default is 10.
Note: The value specified for spinfps may not be possible on the viewer's
platform. Chime will get as close as the system allows.
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Specifies the rotation speed along the X-axis (horizontal axis) in degrees per second. The default is 0 (no spin).
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Specifies the rotation speed along the Y-axis (vertical axis) in degrees per second. The default is 30.
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Specifies the rotation speed along the Z-axis in degrees per second. This is the axis that "comes out of the screen" toward the user. The default is 0 (no spin).
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Specifies what file to open and display. This can be a MOL (MDL molecule) file, a PDB (Protein Databank) file, or an XYZ animation file.
In general, if you use the src tag, you do not
need to also specify an embed type. The embed type
is determined automatically.
Specifies whether, and how, to display disulphide bonds.
off - do not display disulphide bonds
on - display disulphide bonds as dashed lines
number - display disulphide bonds as cylinders
whose diameter is proportional to the number.
Set to true if you want an animation in a concatenated
XYZ file to begin immediately. If false, you can start the
animation using the RasMol script command "animation on".
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Set to true if you want the structure to start spinning
immediately upon loading. If false, you can start the spin
with the RasMol script command "spin".
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Used instead of src to load an in-line compressed
molfile. The compressed molfile is a compressed, URL-safe encoded version
of the structure file. It is generated by Chemscape Server. You must specify
the mime type of the plug-in via the type= tag.
In a Chime button, specifies which Chime structure window should
execute the attached RasMol or CSML script. The other Chime is referenced
according to its name.
Used to specify the mime type of the plug-in when the structure= option is used.
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