SAMSON provides various visualization tools (visual models, visual presets, etc.) and rendering options (styles, special effects, etc.) to help you analyze molecular systems and create beautiful visualizations and animations.
You can try the following interactive tutorials in SAMSON (Help menu > Tutorials): "Visualization: visual models and colorization", "Visualization: rendering parameters".
See also: Selecting, Colorizing, Visual models, Visual presets, Rendering using Cycles, Presenting and animating
In this section, you will learn how to use SAMSON's visualization tools and rendering options.
Prerequisites:
The fastest way to visualize a molecular system is by applying visual presets to it. Visual presets provide an efficient way to apply multiple visual representations and color schemes simultaneously to a complex molecular system based on selectors, all in just a few clicks. 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. See the Visual presets section on how to apply and create visual presets.
To apply a visual preset click on Visualization menu > Visual model > Visual preset and, in the pop-up window, select a visual preset among the existing ones and click apply.
The visual preset is applied to the selected nodes or to the whole document if nothing is selected. The visual models created by the visual preset are stored in the document in a folder named based on the visual preset.
In the example below, the receptor is shown as ribbons, ligands and waters are represented as licorice, and ions are shown through a van der Waals representation in just a few clicks.
Please refer to Visual presets section for more information on how to apply visual presets and create your own visual presets.
Further in this section you will learn how to apply visual models, colorize, and change various rendering effects.
If you would like to apply an illustrative visualization and rendering style inspired by the RCSB PDB Molecule of the Month style by David S. Goodsell (RCSB PDB-Rutgers and The Scripps Research Institute) follow these steps:
To reset the view and the rendering style, remove the applied visual models in the Document view and in Visualization menu > Presets choose Default or High quality as shown in the Changing rendering presets subsection.
SAMSON provides several predefined rendering presets between which you can easily switch in Visualization menu > Presets.
Rendering presets make it possible to quickly switch between different sets of special rendering effects like ambient occlusion, lighting, fog, shadows. You can also easily change these rendering effects in Visualization menu > Options or directly in Preferences as described in the Special effects section.
To save a picture, you can capture the viewport:
You can modify the capture preferences in the Preferences > Interface > Captures panel (Interface menu > Preferences).
You can hide from displaying in the viewport any group of structural nodes (atoms, chains, residues, molecules, etc.), folders, visual models, meshes, labels, and some other nodes. When you hide a parent node its descendants will be automatically hidden as well, e.g. if you hide a residue then atoms in this residue will be hidden, but you can make descendant nodes visible while their parent node is hidden.
You can hide a node just by unchecking the box of this node in the document view. For example, in the image below the chain B is hidden and won't be visible in the viewport. You can show a node by checking the box back.
Note: If at least one descendant of a node is visible then the node's box in the document view will be shown as ticked to depict that some of its descendants are visible.
To change the visibility of nodes, select them in the document view or in the viewport, then in the context toolbar go to the Visibility section where you can change the visibility of the selection and of all nodes. For example, in the image below we are to hide the two selected chains.
Also, you can hide/show nodes using Python Scripting.
For some nodes (structural models, folders, labels, and many visual models, meshes) you can modify their transparency by selecting them and changing this parameter in the Inspector.
Here is how, a semi-transparent structural model might look like along an opaque secondary structure visual representation:
Atoms and bonds in structural models have a default visual representation, where atoms are represented as balls and bonds as sticks.
You can modify it in Preferences > Rendering > Structural models:
Try various options, constant atoms size or atom size proportional to van der Waals radius, and various parameters for atom and bond sizes to see how it affects the display of molecules. If the Automatically test box is checked, this immediately affects the rendering in the viewport.
For example, here is how a molecule looks like with the "Constant atom size" option and the default atom radius (0.3Å):
And here how the same molecule looks like with the "Atom size proportional to van der Waals radius" option.
Visual models provide alternate visual representations of structural models, or even some arbitrary shapes, that may be displayed in the viewport.
Let's open a molecule, e.g. 1AF6 using Home menu > File > Fetch which will download it from RCSB PDB. We will apply a Ribbons (secondary structure) visual model to it.
Important: When a new visual model is added to the document, it is applied to the current selection, or, if nothing is selected, to the whole document. So, before adding a visual model make sure that a system to which you would like to apply it is selected and nothing else is selected, or nothing is selected if you would like to apply it to everything in the document.
Visual models may be added from the Visualization menu (Visualization > Visual model) or via Ctrl / Cmd⌘ + Shift + V . A pop-up menu will appear asking you to choose a visual model type and provide a name for a visual model node that will be created. For example, let's choose the Ribbons (secondary structure) visual model.
As a result, a new visual model will be added in the document. You can also hide the structural model by unchecking its box in the document view.
Provided they handle them, visual models can be colorized with color schemes. This is the case for the Ribbons (secondary structure) visual model which we added before (when no color scheme is applied, a default color scheme based on the residue sequence numbers is used, as in the picture above). For more information see the Colorizing section.
As other node, you can colorize a visual model in several ways:
In the example below, we apply different color schemes to the Ribbons visual model using the above-mentioned ways.
You can apply several visual models at once even to the same nodes. For example, try applying the Licorice visual model: select a molecule, click Ctrl / Cmd⌘ + Shift + V , and choose the Licorice visual model.
See the Colorizing section.
See the Rendering effects section.
Let's make the following image of the molecule with PDB code 3J27 (part of the Dengue virus):
You can reproduce this image via the following steps:
Let's make the following image of the molecule with PDB code 1EQZ (the nucleosome core particle):
You can reproduce this image via the following steps:
Let's reproduce an image of the molecule with PDB code 3JC8 (the type IVa pilus machine in a piliated state).
Here we colorized 3JC8 by groups of chains. Please, download 3JC8.sam file in which for simplicity we combined chains in groups.
You can reproduce this image via the following steps:
Let's make the following image of the molecule with PDB code 4QWE (DNA polymerase in complex with DNA).
You can reproduce this image via the following steps:
atom.symbol S or atom.symbol Ca
(short version: a.s S or a.s Ca
) and click Enter . Now you should see 11 nodes selected, press Ctrl / Cmd⌘ + Shift + V and add Van der Waals visual model. Select in the document view the newly created Van der Waals visual model and in the Inspector (click Ctrl / Cmd⌘ + I if you do not see the Inspector) set the scale to 0.75.Let's make the following image of the molecule with PDB code 1DGF (the human erythrocyte catalase).
You can reproduce this image via the following steps:
n.t structuralGroup
(short version: n.t sg
) and click Enter , then right-click on any selected node, and choose Invert selection in the context menu, then using the context toolbar for the selection choose Visibility > Hide selection. Let's now hide all water atoms: open the Find window, input a.water
and click Enter , then in the context toolbar choose Visibility > Hide selection.See also: Color schemes See also: Visual models See also: Visual presets See also: Presenting and animating