Preferences

To open the Preferences panel: Interface menu > Preferences or Ctrl + K on Windows and Linux or Cmd⌘ + K on Mac.

Preferences are organized in several categories visible on the left side of the panel.

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The preferences panel

If the “Automatically test” check box in the bottom part of the Preferences panel is checked, the changes in preferences immediately affect the interface and rendering.

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Automatically test changes

Editors

Add

In the Editors > Add section of the Preferences panel you may modify the Add editor settings.

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The Add editor preferences

Erase

In the Editors > Erase section of the Preferences panel you may modify the Erase editor settings.

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The Erase editor preferences

Move

In the Editors > Move section of the Preferences panel you may modify the Move editors settings.

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The Move editors preferences

Minimize

In the Editors > Minimize section of the Preferences panel you may modify the settings for the interactive minimization.

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The interactive minimization preferences

Select

In the Editors > Select section of the Preferences panel you may modify the Select editor settings.

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The Select editor preferences

Snapping

In the Editors > Snapping section of the Preferences panel you may modify the snapping settings which are used in some move editors.

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The snapping preferences

Interface

Captures

The preferences for the captures of the viewport may be changed in the Interface > Captures section of the Preferences panel:

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The captures preferences

This section lets you choose the folder in which captures are saved when pressing F10, the prefix used in filenames (prefix to which is appended an integer denoting the capture index), the file format (jpg, png or bmp), and the size (custom, or a multiple of the viewport size).

The “Preserve aspect ratio” box may be checked to maintain proportions when changing the width or the height of the capture.

The “Transparent background” box may be checked to remove the background from the image when saving with the png format.

Dark mode

In the Interface > Dark mode section of the Preferences panel you may switch to the Dark mode version of the interface and back.

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The Dark mode preferences

Menu

In the Interface > Menu section of the Preferences panel you may toggle showing of some specialized menu tabs.

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The menu preferences

Tips

In the Interface > Tips section of the Preferences panel you may modify the tips settings.

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The tips preferences

Windows

In the Interface > Windows section of the Preferences panel you may set the following preferences for the windows: opacity, casting of shadows.

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The windows preferences

Network

Proxy

If you need to specify the proxy settings, you can do it in the Network / Proxy section of the Preferences panel:

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The proxy settings

This settings are useful if you are using a proxy to access the Internet.

Rendering

Ambient occlusion

The ambient occlusion settings may be changed in the Rendering > Ambient occlusion section of the Preferences panel:

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The ambient occlusion settings

Ambient occlusion improves the perception of depth in molecules, by simulating the fact that deeper regions are less accessible to light, and are thus darker.

Two types of ambient occlusion are handled in SAMSON:

  • Screen-space ambient occlusion efficiently provides an approximate simulation, but is sensitive to the distance to the camera.
  • Object-space ambient occlusion is more realistic, but slower.

Even the screen-space ambient occlusion is very useful to improve the depth perception however.

Anti-aliasing

The anti-aliasing settings may be changed in the Rendering > Anti-aliasing section of the Preferences panel:

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The anti-aliasing settings

Anti-aliasing removes jagged edges from images and may significantly improve rendering.

Fast Approximate Anti-Aliasing (FXAA) is typically very efficient and can be activated on most recent graphics cards.

Background

The background of the viewport may be changed in the Rendering > Background section of the Preferences panel:

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The background color settings

Four options are available:

  • SAMSON: the default SAMSON background
  • Black: an entirely black background
  • White: an entirely white background
  • Custom: a gradient from a user-defined top color to a user-defined bottom color

Bloom

The bloom settings may be changed in the Rendering > Bloom section of the Preferences panel:

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The bloom settings

The Bloom effect adds a controllable “halo” around the brightest parts of the image to simulate imaging artefacts, which may add realism to images.

Cameras

The cameras settings allows you to switch on/off the orthographic projection (it can also be modified for a camera in the inspector):

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The cameras settings

Depth-of-field

The depth-of-field settings may be changed in the Rendering > Depth-of-field section of the Preferences panel:

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The depth-of-field settings

This effect simulates the depth-of-field effect produced by actual cameras (e.g. blurred distant objects). If enabled, when you zoom on the molecule its distant parts will be blurred.

Fog

The fog settings may be changed in the Rendering > Fog section of the Preferences panel:

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The fog settings

Basically, fog makes distant objects less visible. Fog attenuates distant parts by blending them progressively with the background. Turn it on to make it easier to focus on the foreground.

The near and far distances are based on the camera location and determine where the fog is enabled. Before the "near distance" there is no fog, after the "far distance" every node is invisible. The "strength" parameter influences the speed at which the fog is appearing.

Grid

The grid settings may be changed in the Rendering > Grid section of the Preferences panel:

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The grid settings

Labels

The labels preferences may be changed in the Rendering > Labels section of the Preferences panel:

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The labels preferences

You can specify the font for labels and the number of decimal places for angles and distances shown in labels.

Lighting

The lighting parameters may be changed in the Rendering > Lightning section of the Preferences panel:

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The lighting parameters

This section makes it possible to control the parameters of the two point lights that illuminate the document, as well as global parameters. Each light has the following parameters:

  • Light color: click the square to change the color of the light
  • Light intensity (between 0 and 1): the intensity of the light
  • Specular intensity (between 0 and 1): the intensity of the light reflection on surfaces. High values make surfaces look like plastic, while low values make surfaces look matte.
  • Specular power (between 0 and 1000): the decay of specular reflection. High values produce sharper specular reflections.
  • Longitude and latitude control the position of the light.

The first light is typically the main light, which is thus typically brighter than the second light (a “back light”).

Finally, three more parameters are global:

  • Fresnel intensity (between 0 and 1): the amount of background light reflected at grazing angles
  • Fresnel power (between 0 and 100): how fast the Fresnel effect decays
  • Ambient light: the amount of light that reaches objects, even when the intensity of both lights is set to 0.

Pinhole

The pinhole settings may be changed in the Rendering > Pinhole section of the Preferences panel:

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The pinhole settings

The Pinhole effect simulates looking through a pinhole, which may be useful when you want to focus attention on the center of the image (for example, a ligand followed by the camera using the new Follow atoms animation).

Presentations

The presentations settings may be changed in the Rendering > Presentations section of the Preferences panel:

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The presentations settings

Selection

The selection preferences may be changed in the Rendering > Selection section of the Preferences panel:

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The selection preferences

You can specify the color of selection, its opacity, and to show or not the selection box.

The highlighting color is the color which is used to highlight the node over which you hover in SAMSON. This helps you see what nodes will be selected.

The outline color is the color which used to colorize the outline of the highlighted or selected nodes. You may set the opacity of the outline to zero to increase the graphics performance and eliminate some lags on old graphics cards.

Shadows

The shadows settings may be changed in the Rendering > Shadows section of the Preferences panel:

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The shadows settings

Shadows are particularly helpful to improve the perception of relative positions. Without shadows, it may be difficult to perceive the relative positions.

In case of an old graphics card you may want to either disable this option, or choose the lower preset.

Silhouettes

The silhouettes settings may be changed in the Rendering > Silhouettes section of the Preferences panel:

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The silhouettes settings

Silhouettes make it easier to separate regions with different depths. Turn on silhouettes to produce clearly delineated structures.

Scale

The scale settings may be changed in the Rendering > Scale section of the Preferences panel:

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The scale settings

Stereo

The stereo view preferences may be changed in the Rendering > Stereo section of the Preferences panel:

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The stereo view preferences

Stereo settings are applied to the stereo view (3D glasses).

Structural model settings

The atom radius and bond radius may be changed in the Rendering > Structural models section of the Preferences panel:

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The structural model settings

Installation

General

The general installation info can be viewed in the Installation > General section of the Preferences panel:

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The general installation info

The general installation info shows the following:

  • Your user type (User / Developer)
  • E-mail address used for registration on SAMSON Connect
  • Information on your graphics cards
  • Frequency of update checks
  • Information on the SAMSON Installation (the SAMSON key, the SAMSON version, the location, and the installation date)
  • For a developer, information on the SAMSON SDK Installation (the SAMSON SDK key, the SAMSON SDK version, the location, and the installation date)

Updates

The updates installation info can be viewed in the Installation > Updates section of the Preferences panel:

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The updates info

This page shows the availability of updates for SAMSON, SAMSON SDK and SAMSON Extensions, the current versions installed, and a possibility to check the detailed information on the installed SAMSON Extension by clicking the "Details" button which should open a web-page associated with this SAMSON Extension.

In case if you are a developer, this page also shows information on the SAMSON Extensions developed and installed by you locally. You can uninstall them by pressing the "Uninstall" button.

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Information on the developed SAMSON Extensions