Edit Custom Preset Dialog Box

Edit a custom preset for styling the Workspace structures.

To open this dialog box: click the Edit button in the Manage Custom Presets Dialog Box.

Using the Edit Custom Preset Dialog Box

Setting the custom style involves selection of options for the style elements that are modified by application of the custom preset, and making settings for how to change the style for that style element. For example, in the General tab, you can select an option for the display of ligands. If you select this option, application of the preset may modify the visibility of ligands; if you deselect it, no changes are made to the visibility of ligands. After selecting the option, you choose whether you want the ligands to be shown or hidden. So if you select the Ligands option and choose none from the option menu, the ligand is hidden when the preset is applied. If you deselect the Ligands option and the ligand is visible, it remains visible when the preset is applied.

The preset style is applied to all atoms in the Workspace that are not in locked entries. So if you want to keep the style of some entries the same even when the preset is applied, you can lock them to prevent any changes being made.

Edit Custom Preset Dialog Box Features

Preset options
Name text box
Name of the preset.
Workspace default option
Make the preset the default for displaying structures in the Workspace. Selecting this option overrides the previous default.
General tab

Set general display options: display of atoms, fitting of the Workspace.

Display atom section

Select options for changes to the display of atoms when the preset is applied.

Ligands option and menu

Select this option to change the visibility of ligands, and choose from all (display all ligands) or none (hide all ligands).

Residues option, menu, and box

Select this option to change the visibility of protein residues, and choose which residues to display from the option menu:

  • all—display all protein residues.
  • within—display residues within a given distance of the ligand, and specify the distance in the text box that is displayed.
  • none—do not display any protein residues.
Waters option, menu, and box

Select this option to change the visibility of water molecules, and choose which waters to display from the option menu:

  • all—display all water molecules.
  • within—display water molecules within a given distance of the ligand, and specify the distance in the text box that is displayed.
  • none—do not display any water molecules.
Ions option, menu, and box

Select this option to change the visibility of ions, and choose which ions to display from the option menu:

  • all—display all ions.
  • within—display ions within a given distance of the ligand, and specify the distance in the text box that is displayed.
  • none—do not display any ions.
Receptor hydrogens option and menu

Select this option to change the visibility of receptor hydrogens, and choose which ones to display from the option menu:

  • all—display all hydrogens.
  • polar only—display only the polar hydrogens on the receptor.
  • none—do not display any hydrogens.
Ligand hydrogens option and menu

Select this option to change the visibility of ligand hydrogens, and choose which ones to display from the option menu:

  • all—display all hydrogens.
  • polar only—display only the polar hydrogens on the ligand.
  • none—do not display any hydrogens.
Fit to ligand option

Zoom in so that the ligand fills most of the Workspace.

Representation tab

Set options for changes to the atom and ribbon representations. For information on setting the parameters of the representations, see the Molecular Representation Preferences description in the Preferences Panel topic.

Representation section

Change the atom and bond style to one of the five available styles: wire frame, tube, thin tube, ball and stick, and CPK.

Default option and menu

Change the default atom and bond style to the menu choice. This style is applied to protein residues, and anything else that is not specified below.

Ligands option and menu

Change the atom and bond style for the ligands to the menu choice.

Waters option and menu

Change the atom and bond style for water molecules to the menu choice.

Ions option and menu

Change the atom and bond style for ions to the menu choice.

Ribbons section

Set up the changes to the display of ribbons to be made when the preset is applied.

Display option and menu

Select this option to change the ribbon display , and choose which parts of the ribbons to display from the option menu:

  • all—display the entire ribbons (the default).
  • within—display parts of the ribbons that are within a given distance of the ligand, and specify the distance in the text box that is displayed.
  • none—do not display any ribbons.

Note that the display of ribbons and the display of the corresponding protein atoms are independent.

Scheme menu

Choose the color scheme for the ribbons. This option menu provides a range of properties that can be used to select the color scheme, such as residue properties and secondary structure. Each of these has a predefined set of colors that is applied to the ribbon, coloring the corresponding segments for each residue. The color schemes are explained in Coloring Atoms.

Style menu

Choose the ribbon style from one of the seven display styles: Cartoon, Ribbon, Tube, Thin Tube, Curved Line, Calpha Line, and Calpha Tube. You can also choose None to undisplay ribbons.

Color tab
Color schemes section

Set up changes to the atom color scheme to be made when the preset is applied. The color schemes are explained in Coloring Atoms.

Default option and menu

Change the default atom color scheme to the menu choice.

Ligands option and menu

Change the atom color scheme for the ligands to the menu choice.

Waters option and menu

Change the atom color scheme for the waters to the menu choice.

Ions option and menu

Change the atom color scheme for the ions to the menu choice.

Labels tab
Label atoms section

Set up changes to the atom labels to be made when the preset is applied. The same choices are available on each option menu. Choosing Current Composition allows you to use a custom label, which you can set up by choosing Edit Custom Label from the Apply Labels menu in the Style toolbox. Choosing None removes labels.

Protein option and menu

Change the atom labels for the proteins to the menu choice.

Ligands option and menu

Change the atom labels for the ligands to the menu choice.

Waters option and menu

Change the atom labels for the waters to the menu choice.

Ions option and menu

Change the atom labels for the ions to the menu choice.

Interactions tab

Set options for changing the display of noncovalent interactions and contacts when the preset is applied. The criteria for these interactions and contacts can be set in the Nonbonded Interactions Preferences of the Preferences Panel.

Display chosen interactions option

Change the display to show or hide the interactions that are selected below. The options for the interactions are only displayed when this option is selected. Selecting one of the options shows the interaction; deselecting it hides the interaction. If you select any of the options, an option menu is displayed so you can choose the parts of the structure that the interaction is displayed between.

H-bonds and halogen bonds options

Select options for display of hydrogen bonds, halogen bonds, salt bridges, and aromatic hydrogen bonds

Contacts options

Select options for display of good, bad, or ugly contacts.

Pi interactions option and menu

Select options for the display of pi-pi stacking and pi-cation interactions.

Surfaces tab

Set options for changing the display of molecular surfaces when the preset is applied. These options do not affect the display of other surfaces that are based on calculated 3D properties, such as the electron density.

Display chosen molecular surfaces option

Select this option to change the display of receptor and ligand molecular surfaces when the preset is applied. The options for the surfaces to display are only displayed when this option is selected. Selecting one of the options shows the surfaces; deselecting it hides the surfaces. If the surface does not exist, it is created.

Receptor option

Change the display of receptor surfaces. When you select this option, the following controls are displayed:

  • all and within options—specify which part of the receptor to display the surface for. If you choose within, specify the maximum distance from the ligand for the surface for a residue to be displayed. If the residue has any atom within this distance of a ligand atom, the surface is displayed. If it is created, it is an open surface.
  • Transparency box—set the transparency of the surface.
  • Color scheme option menu—Choose a color scheme for the surface. The surface is colored according to the property of the nearest atom.The color schemes are explained in Coloring Atoms.
Ligands option and menu

Change the display of ligand surfaces. When you select this option, the following controls are displayed:

  • Transparency box—set the transparency of the surface.
  • Color scheme option menu—Choose a color scheme for the surface. The surface is colored according to the property of the nearest atom.The color schemes are explained in Coloring Atoms.
Action buttons
Apply Now button

Apply the current settings in the panel to the Workspace structure. This allows you to preview the settings at any time during the process of building up a preset style.

Note that applying the settings does not save them, which you do with the Save button.

Save New button

Save the settings as a new named custom preset, and keep the dialog box open for further edits. The Save as Custom Preset dialog box opens, so you can name the new preset, and also choose to set it as the Workspace default. Once you have saved the preset, you can continue working in the dialog box to create other presets. This is useful if you want to create several similar presets with small variations.

Save button

Save the settings to the named preset, and close the dialog box. Saving the settings does not apply the preset, which you can do with the Apply Now button before you save.

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