Visual presets

The fastest way to visualize a molecular system is by applying visual presets to it. Visual presets are powerful way to apply multiple visual representations and color schemes simultaneously to a complex molecular system, all in just a few clicks.

Visual Presets are accessible from both the Visualization menu and the Home menu.

SAMSON provides a set of default visual presets and you can create and save your own visual presets, e.g., by modifying the existing ones.

Applying visual presets#

Click on Home > Visual preset or Visualization > Visual preset and choose a visual preset among the existing ones.

Visual presets menu

Here is how the Protein-ligand preset looks like on PDB code 1AA1:

Applying a visual preset

Note

The visual preset is applied to the selected nodes or to the whole document if nothing is selected. When visual preset is applied, it creates a folder in the document with a name corresponding to this visual preset, and puts there visual models created by the visual preset and node groups corresponding to the selections.

Creating visual presets#

Visual Presets can be easily customized or created from scratch, with any number of steps, using the Visual Preset Editor.

Visual presets window

Each Visual Preset consists of a series of steps, and each step is composed of four choices:

A selection of nodes to which the step applies (e.g., "Receptor", "Ligands", "Heavy atoms and polar atoms in ligands")
An optional set of actions applied to the selection (e.g., "Hide", "Label atoms", "Zoom on selection", etc.)
An optional visual model applied to the selection (e.g., "Van der Waals", "Licorice", "Ribbons", etc.)
An optional color scheme applied to the selection or the visual model (if added) (e.g., "Per chain", "Per occupancy", "Constant", etc.)

You can create and save your own visual presets either by modifying the existing ones or by creating a new one from scratch. Your saved visual presets will be loaded along with the default ones every time you launch SAMSON allowing you to create visualizations and images in the style you want in just a few clicks.

To create a new visual preset go to Home > Visual preset > Create... or Visualization > Visual preset > Create....

If you want to create a visual preset based on an existing one, then simply choose it from the list and start modifying, e.g. by adding/removing visual preset steps, changing selections, visual models, color schemes, color palettes.

If you want to create a visual preset from scratch, then click on the plus button add icon next to the list of the existing visual presets.

Add a new visual preset

Then click on the add icon Add step button below to add a new visual preset step.

Add a new step to the visual preset

Let's now choose for what types of nodes this step should be applied. There is a number of default options, e.g.: "Receptor", "Ligands", "Water", etc. By default, when you add a new visual preset, it is set to Any node which means that this step will be applied to the whole document if nothing was selected or to the current selection to which the visual preset is applied.

Choose a selection

If you don't find a suitably selection in the list, you can create your own. For that, scroll down the list and click on add icon More... - this will open the Find window in which you can compose the selection using the Node Specification Language.

You can apply various actions to the selection (e.g.: "Hide", "Label atoms", "Zoom on selection") - click on add icon in the Apply actions row:

Choose an action

You can add multiple actions in a single step - they will be applied in the order they've been added. To remove an action, simply hover above it and click on X that will appear in its top-right corner:

Remove an action

If you want you can choose a visual model from the list.

Choose a visual model

If you want you can choose colorization: no colorization, constant color, per element colorization, and different per-attribute color schemes.

Choose a colorization

Note

If no colorization is chosen and there is a visual model specified then the visual model will have its default colorization.

If no visual model is chosen then the colorization, if specified, is applied to the structural nodes determined by the selection.

If a colorization is chosen, then its default color palette (or just a color for constant colorizations) will be shown in the same row. If you want to modify the color palette, then double-click on it and choose (or create one) in the pop-up Choose color palette... dialog. If a constant color was chosen as a color scheme, then you can modify the color by double-clicking on it.

Choose a color palette

You can always return to the default color palette associated with the chosen color scheme by double-clicking on the color palette field and selecting the Default color palette in the Choose color palette... dialog.

If you want to delete a step from the visual preset, then click on the visual preset step line and then click on the minus icon Delete step button.

You can also change the order of steps via the Move up and Move down buttons.

If you want to save your custom visual presets click on the Save visual preset button or simply click on the Apply button to apply it and you will be asked whether you want to save it or not.

Would you like your visual presets to be added to the list of default visual presets in SAMSON? Then please contact us using the Send feedback button in the top-right part of SAMSON.