Editors Collection

Publisher: OneAngstrom

Updated: August 11, 2022


Latest versions

4.1.1 for SAMSON 2022 R2

4.1.1 for SAMSON 2022 R2

4.1.0 for SAMSON 2022 R2

Included with all plans

Editors Collection

Publisher: OneAngstrom

Updated: August 11, 2022


Latest versions

4.1.1 for SAMSON 2022 R2

4.1.1 for SAMSON 2022 R2

4.1.0 for SAMSON 2022 R2

A collection of editors to build, modify, move, measure, and label molecular systems.

You can find editors in can the Edit group of the Home menu or in the Edit menu or in the Editors menu.

Select

The Select editor (shortcut: R) allows you to select nodes by clicking on them or using a rectangle selection.

Select editor

Note: the level of selection depends on the current Selection filter.

See: User guide: Selecting.

Add

The Add editor (shortcut: A) allows you to build molecular systems by adding and connecting atoms and fragments provided with assets.

SAMSON provides you with the possibility to build using individual atoms from the Edit menu or Quick access commands...

Build using atoms

or using the Periodic table...

Build using the Periodic Table

or you can build by assembling assets.

Build using assets

See: User guide: Building molecules

Bond order

Change bond order using the Bond order editor (shortcut: B). Hover over bonds and click their controllers to increase and decrease their order.

Change bond order

See: User guide: Changing bond order

Atom charge

Change the atom's formal charge using the Atom charge editor (shortcut: C). Hover over atoms and click their controllers to increase and decrease their formal charge.

Change atom formal charge

See: User guide: Changing atom formal charge

Move

Move editors provide you with precise control over positions and orientations of molecules.

Move editor example

You can change the pivot point.

Move editor example

You can move and rotate parts of molecules.

Move editor example

You can move object with or without snapping. You can modify the snapping preference in the Edit menu > Snapping, in the editor's Quick access menu in the top-right corner of the Viewport, or in the Preferences..

There are several Move editors:

The displacer editor (shortcut: D).

This simple move editor allows you to displace nodes in the plane of the screen. You can either displace currently selected nodes by pressing on them and dragging or press on another node and drag it. In the later case, the selection is based on the current Selection filter. This editor is particularly useful when performing interactive simulations.

The local move editor (shortcut: M).

Translate or rotate the selected atoms along the principal axes of the selected atoms:

Use the central translation widget to move atoms in the plane of the camera. Use the side translation widgets to move atoms along the principal axes of the selected atoms. Use the side rotation widgets to rotate atoms around the principal axes of the selected atoms. Use the trackball widget to rotate atoms freely.

Important: right-click (or press Ctrl/ Cmd⌘ and left-click) on widgets to enter a precise displacement or angle. Right-click on translation widgets to align atoms along global axes.

The global move editor (shortcut: K).

Acts as the local move editor but in global XYZ coordinates.

The minimal move editor (shortcut: J).

A minimal version of the local move editor without some controllers.

The simple move editor (shortcut: H).

Use the translation widget to move atoms in the plane of the camera.

See: User guide: Move editors

Measure

Measure distances, angles, and dihedrals (shortcut: Ctrl/Cmd⌘+M).

Measure editor example

Click on a bond to toggle displaying its length.

Click on two atoms to display the distance between the atoms.

Click on three atoms to display the angle between the atoms.

Click on four atoms to display the torsion between the atoms.

To save the displayed data as a label in the document, press Enter.

See: User guide: Measuring.

Label

Left-click on a node (atom, bond, residue, etc.) to display its name. Right-click to give a custom label to the clicked node or the current selection or to label various nodes in the selection.

Label editor example

Use the Selection filter to control what is being labeled.

You can change the default label font in Preferences > Rendering > Labels.

Label rendering preferences

You can also change the font for labels using the Inspector.

See: User guide: Labeling.

Erase

Delete nodes by clicking on them in the Viewport using the Erase editor (shortcut: E).

Note: the erase node level depends on the current Selection filter.

Editors Collection is an extension for SAMSON,
the integrated platform for molecular design.

To use Editors Collection:

1. Create your free account and choose a molecular design plan
2. Download and install SAMSON on your computer


When you restart SAMSON, the extension will be automatically installed
and will be usable directly from within SAMSON.