Manually changing the applet code

There are several PARAM tags you can add to customize the JMV applet's appearance. Please note that in HTML code that has already been modified to use the Java Plug-In, these applet parameters must be added in 3 places in order to be effective:

1. Once as <PARAM NAME = name VALUE=value> after the <OBJECT> tag.
2. Once as <... name = value ...> within the <EMBED...> tag.
3. Once again as <PARAM NAME = name VALUE = value> after the <APPLET> tag.

The available JMV applet parameters are listed below.

• FILE:
  If the FILE parameter is not null, then JMV will start by displaying the specified molecule. This is necessary if the LOADBUTTON or CONTROLS parameters are set, since there would be no other way to load a molecule. The file must be publicly available if others are to view it.

• SEPARATE_WINDOW:
  If the SEPARATE_WINDOW parameter is ``true'', then the molecule window will appear in a separate frame, instead of within the webpage. This is useful because the new window is resizable.

• LOADBUTTON:
  If the LOADBUTTON parameter is ``false'', then the ``Load a file'' option in the ``File'' menu will not be displayed. This is useful if you want the user to view a molecule, and change colors and representations, but not change the molecule being viewed.

• CONTROLS:
  If the CONTROLS parameter is ``false'', then the menu will not be shown. Only the molecule window will be shown. This is useful if you want to display a molecule with a given representation and color, and not allow those to be changed, or to make the applet present itself with no controls for aesthetic reasons.

• REP:
  If the REP parameter is set, JMV will display the initial molecule with the given rep. These are the current representation options:
  

  1: Lines
  2: VDW
  3: Bonds
  4: CPK
  5: Trace
  6: Tube
  7: Licorice
  

• COLOR:
  If the COLOR parameter is set, JMV will display the initial molecule with the given color scheme. These are the current options:
  

  0: color by name
  1: color by index
  2: color by residue name
  3: color by chain
  4: color by segment name
  5: color by structure
  

• GRADIENT:
  If the GRADIENT parameter is set, JMV will display the initial molecule with the given color gradient. These are the current options:

  0: Red$\rightarrow$Green$\rightarrow$Blue
  1: Blue$\rightarrow$Green$\rightarrow$Red
  2: Red$\rightarrow$White$\rightarrow$Blue
  3: Blue$\rightarrow$White$\rightarrow$Red
  4: Black$\rightarrow$White
  5: White$\rightarrow$Black
  

• WINHEIGHT:
  The WINHEIGHT parameter specifies the height of the molecule window. If not specified, the default is 400.

• WINWIDTH:
  The WINWIDTH parameter specifies the width of the molecule window. If not specified, the default is 400.

• PUBSYNCH:
  If the PUBSYNCH parameter is set to FALSE, the ``Load session'' and ``Save session'' options will not be shown in the ``File'' menu.

• HELPPAGE:
  You can set the HELPPAGE parameter with the value of a URL to display when the ``JMV Help'' option under the ``Help'' menu is chosen. It defaults to the help page on the main JMV site.

Two additional parameters that can be specified are HEIGHT and WIDTH. These are specified within the APPLET tag. These parameters control the height and width of the applet itself. The default dimensions are 400 for height and 400 for width.