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Tag name: altscript
Description: Specifies 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.
Syntax: altscript={RasMol script commands}
See also: button, buttonstate, script
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Tag name: animfps
Description: 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.
Syntax: animfps={animation events per second}
See also: AnimFrameCallback, animmode, startanim |
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Tag name: AnimFrameCallback
Description: Specifies the name of a JavaScript function in the current document that is to be called before each events ("frame") of an animation (.xyz) file is displayed. The function should conform 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 the frameNumber is an integer indicating which number event in the file is about to be displayed.
Syntax: AnimFrameCallback={JSFunctionName}
See also: animfps, animmode, startanim |
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Tag name: atommapnum2d
Description: An atom-atom map on the reaction components specifies exactly which atoms in the reactants correspond to the atoms in the products. Applies to reactions in 2D
Syntax: atommapnum2d={off|on}
off - do not display atom-atom maps
on - display atom-atom maps
See also: invretmarks2d, reactingcenters2d
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Tag name: bgcolor3d
Description: Sets the background color for 3d rendering
Syntax: bgcolor={black|white|#rrggbb}
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
See also: color2d, palette |
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Tag name: bondlen2d
Description: Specifies the standard bond length, in decipoints, used to display a 2D image when using the tag bondscaling=stdbond. The default length is 180
Syntax: bondlen2d={###}
See also: bondscale2d |
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Tag name: bondscale2d
Description: Specifies the type of scaling to use when displaying a 2D image
Syntax: bondscale2d={asdrawn|asdrawn_fitbox|fixbox|stdbond}
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.
See also: atomnum2d, bondlen2d, fontsize2d, fontname2d, hlabels2d |
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Tag name: buttonstate
Description: 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".
Syntax: buttonstate={pushed}
See also: altscript, button
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Tag name: ButtonCallback
Description: This tag is only 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 executeYet? is false when JSFunctionName is first called (before execution of the script) and the true the second time.
With the LiveConnect interface in Chime, 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. You can also see an example of the LiveConnect interface in "Using LiveConnect" under the Tutorials section.
Syntax: ButtonCallback={JSFunctionName}
See also: button, csml, immediate, script
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Tag name: color3d
Description: Specifies the color scheme for 3D display
Syntax: color3d={chain|cpk|group|monochrome|shapely|structure|temperature|user}
The options correspond to those available in the Chime menu.
See also: bgcolor, display3d, option3d, palette, scale3d |
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Tag name: csml
Description: 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
Syntax: csml={valid CSML script commands}
See also: button, immediate, script, target |
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Tag name: debugscript
Description: When debugscript=true, each line of an executing Rasmol script is echoed to the browser's status line.
Syntax: debugscript={false|no|true|yes}
false or no - do not echo script commands true or
yes - echo script commands to status line
See also: script |
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Tag name: display2d
Description: 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.
Syntax: display2d=true
See also: color2d, display3d
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Tag name: display3d
Description: Specifies the type of 3D display
Syntax: display3D={backbone|ball&stick|cartoons|ribbons|spacefill|sticks|strands|wireframe}
The options correspond to those available in the Chime menu.
See also: color3d, display2d, options3d, scale3d |
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Tag name: expandResidues2d
Description: Specifies wether to display expanded or contracted residues in Chime Pro is the contracted (in Chime Pro 2.0 the default was the expanded form).
Syntax: expandResidues2d = {on|off}
on - Display expanded residues
off - Do not display expanded residues (default) |
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Tag name: exportV3000
Description: Set to true if you want to export a Chime structure into a V3000 molfile. By default, when you save a Chime
structure to a file, copy it to the clipboard, or transfer it to ISIS/Draw, Chime(or Chime Pro) exports the
structure into a V2000 molfile. The exportV3000 tag only applies to V3000 molfiles. It does not convert V2000
molfiles into V3000 molfiles.
A V3000 molfile is an extended molfile format that consists of a regular molfile "no structure", followed by
a single molfile appendix that contains the body of the connection table (Ctab). For more information about the
extended molfile format or the V3000 molfile, see MDL File Formats in the Download Center at www.mdli.com.
A newer version of the V3000 molfile uses new tags which are not supported by the earlier versions of
ISIS/Draw (version 2.3 and earlier). The new V3000 molfile tags include the COLLECTION tag which is used for new
features such as structure highlighting. To enable structure highlighting in a V3000 molfile, set
color2d=sketch. See the embed tag color2d.
From the Chime (or Chime Pro) plug-in, you can save a V3000 molfile that contains new V3000 tags by setting
exportV3000 to true. However, if you transfer or open this V3000 molfile in an earlier version of ISIS/Draw,
ISIS/Draw cannot display it.
The V2000 molfile is the format that is used in the earlier versions of ISIS/Draw. If you set exportV3000 to
false or if you do not use exportV3000, you can display a V3000 molfile in the Chime(or Chime Pro) plug-in, and
transfer the structure to an earlier version of ISIS/Draw. If you set exportV3000 to true for a V2000 molfile,
the structure remains as a V2000 molfile.
Syntax: exportV3000={true|false}
See also: color2d
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Tag name: fontsize2d
Description: Sets the font size, in decipoints, used to display atom symbols and other text in 2D display. The default size is 120.
Syntax: fontsize2d={###}
See also: atomnum2d, bondscale2d, fontname2d, hlabels2d |
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Tag name: frank
Description: When frank = true, the "MDL" trademark is displayed in the lower right corner of the Chime structure window
Syntax: frank ={false|no|true|yes}
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Tag name: hbonds2d
Description: Specifies whether, and how, to display hydrogen bond.
Syntax: hbonds2d={off|on|number}
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
See also: ssbonds
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Tag name: hlabels2d
Description: Specifies how to display implicit hydrogen in a 2D structure
Syntax: hlabels2d={asdrawn|false|hetero|terminalhetero|true}
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
See also: atomnum2d, bondscale2d, bondlen2d, fontsize2d, fontname2d
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Tag name: immediate
Description: 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 writting a
Chime button (to an unseen part of the screen) that will execute immediately
to perform some operation on a Chime structure window |
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Tag name: invretmarks2d
Description: Inversion marks specify that a stereo center must be inverted by the reaction. Retention marks specify that a stereo center must retain its configuration. Applies to reactions in 2D
Syntax: invretmarks2d={off|on}
off - do not display the stereochemical changes that are apparent
in reactions
on - display the stereo chemical changes that are apparent in
reactions
See also: atommapnum2d, reactingcenters2d
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Tag name: jcamp_blocknum
Description: For BLOCK or NTUPLE JCAMP-DX files specifies which data set to initially display.
Syntax:
jcamp_blocknum={1...n}
Integer value - display that data set
See also:
jcamp_grid,
jcamp_revplot,
jcamp_help |
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Tag name: jcamp_grid
Description: Specifies whether to display a grid on the JCAMP-DX data
Syntax: jcamp_grid={false|true}
false - do not display grid
true - display grid
See also:
jcamp_blocknum,
jcamp_revplot,
jcamp_help |
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Tag name: jcamp_help
Description: Specifies whether to turn on/off the JCAMP-DX interpret mode
Syntax: jcamp_help={false|true}
false - set interpret off
true - set interpret on
See also:
jcamp_blocknum,
jcamp_grid,
jcamp_revplot |
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Tag name: jcamp_revplot
Description: Specifies whether to reverse the JCAMP-DX plot
Syntax: jcamp_revplot={false|true}
false - do not reverse JCAMP-DX plot
true - reverse JCAMP-DX plot
See also: jcamp_grid, jcamp_help |
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Tag name: LoadStructCallback
Description: Specifies the name of a JavaScript function in the current document that is to be called whenever the user pastes or transfers a structure or opens a file into a Chime Pro query form box. The function should conform to the prototype:
function JSFunctionName(pluginName)
where pluginName is the name specified for the Chime structure window.
Syntax: LoadStructCallbback={JSFunctionName}
Note that if you are using frames you should explicitly specify the
document containing the function, for example:
LoadStructCallback=parent.frameName.MyLoadStructCallback |
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Tag name: messages3d
Description: If true, messages generated by normal operation of Chime's 3D rendering engine are echoed to the browser's status line
Syntax: messages3d={false|no|true|yes}
false or no - do not echo messages
true or yes - echo messages to status line
See also: MessageCallback |
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Tag name: MessageCallback
Description: 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:
function JSFunctionName(pluginName, messageText)
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:
MessageCallback=parent.frameName.MyCallBack
Syntax: MessageCallback={JSFunctionName}
See also: message3d |
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Tag name: name
Description: 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.
Syntax: name={name}
See also: button, ButtonCallback, target |
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Tag name: nmrpdb
Description: Sets the MIME type to the NMR pdb mime type so that "multi-frame" pdb files can be loaded
Syntax: nmrpdb={false|true|auto}
false - use default PDB file reading, even if there are MODEL
records present
true - treat the PDB file as an NMR model and ignore all CONECT
records
auto - treat the PDB file as an NMR model if a MODEL record is
found |
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Tag name: nomenus
Description: Specifies whether to display Chime menus. This feature allows you to turn off Chime's menus except the About menu.
Syntax: nomenus={true|false}
true - do not display Chime menus except for the About menu
false - display all Chime menus |
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Tag name: options3d
Description: Specifies 3D display options. If more than one options3d is specified for the EMBED tag the options will be combined.
Syntax: options3d={dots|hetero|hydrogen|labels|shadows|slab|specular|stereo}
The options correspond to those available in the Chime menu
See also: color3d, display3d, scale3d |
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Tag name: palette
Description: "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
Syntax: palette={background|forground}
See also: bgcolor, color3d |
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Tag name: preloadscript
Description: 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 ";".
Syntax: preloadscript={RasMol script commands}
See also: immediate, script |
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Tag name: PauseCallback
Description: 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
Syntax: PauseCallback={JSFunctionName} |
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Tag name: PauseCallback
Description: 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 faulse when execution of the script resumes
Syntax: PauseCallback={JSFunctionName} |
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Tag name: PickCallback
Description: 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 must 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.
Syntax: PickCallback={JSFunctionName} |
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Tag name: reactingcenters2d
Description: Reacting centers indicate where specific transformations occur on a reaction. Applies to reactions in 2D
Syntax: reactingcenters2d={off|color|thicken|hash}
off - do not display reacting centers
color - display reacting centers in color
thicken- display reacting centers thickened
hash - display reacting centers with hashes
See also: atommapnum2d, invretmarks2d |
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Tag name: scale3d
Description: 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
Syntax: scale3d={real value}
The value should be at least 10 angstroms/inch. The higher the scaling
value, the smaller the molecule will appear.
See also: color3d, display3d, options3d, scale3d |
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Tag name: script
Description: 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.
Syntax: script={valid RasMol script commands}
See also: altscript, csml, debugscript, immediate, preloadscript, target |
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Tag name: sendmouse
Description: Specifies whether to send Chime's mouse events to another target Chime plug-in
Syntax: sendmouse={false|true}
false - do not send mouse events to another target Chime plug-in
true - send mouse events to another target Chime plug-in
Tag name: spinX
Description: Specifies the rotation speed along the X-axis (horizontal axis) in degrees per second. The default is 0 (no spin)
Syntax: spinX={degrees per second}
See also: spinfps, spinY, spinZ, startspin |
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Tag name: spinY
Description: Specifies the rotation speed along the Y-axis (vertical axis) in degrees per second. The default is 30
Syntax: spinY={degrees per second}
See also: spinfps, spinX, spinZ, startspin
Tag name: spinZ
Description: 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)
Syntax: spinZ={degrees per second}
See also: spinfps, spinX,
spinY, startspin |
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Tag name: src
Description: 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
Syntax: src={file name}
See also: structure
Tag name: ssbonds
Description: Specifies whether, and how, to display disulphide bonds.
Syntax: ssbonds={off|on|number}
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.
See also: hbonds |
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Tag name: startanim
Description: 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".
Syntax: startanim={false|no|true|yes}
See also: animfps, AnimFrameCallback, animmode
Tag name: startspin
Description: 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".
Syntax: startspin={true|yes|false|no}
See also: spinfps, spinX, spinY, spinZ |
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Tag name: structure
Description: 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
Syntax: structure={compressed molfile}
See also: src, type |
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Tag name: target
Description: 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.
Syntax: target={target Chime name}
See also: button, csml, immediate, name, script |
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Tag name: type
Description: Used to specify the mime type of the plug-in when the structure = option is used.
Syntax: type={Chime_mime_type}
See also: structure |
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Tag name: version
Description: Specifies the release version of MDL Chime
Syntax: script="show version" |
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