After almost a year of hard work since the previous release, we are proud to announce that SAMSON 0.6.0 is now available for Windows, Linux and Mac, and can be obtained from SAMSON Connect at https://www.samson-connect.net !
Here’s an overview of some of the most prominent new features of the core of SAMSON (separate posts will cover new SAMSON Elements):
SAMSON needs to reach the SAMSON Connect website during installation, and when installing and removing SAMSON Elements. This was difficult for users behind a proxy. Fortunately, it is now possible to configure the proxy during installation (enter your proxy settings when prompted during installation) or while using SAMSON (Go to Preferences). The proxy can be turned on and off when the network configuration changes.
SAMSON is now able to update itself, either by periodically checking for updates on SAMSON Connect, or manually. Go to Preferences to manage updates, as well as the SAMSON Elements that were installed from SAMSON Connect or developed locally.
It is now possible to precisely control what is being picked in the viewport thanks to Selection filters. Selection filters are Node Specification Language (NSL) expressions, and can thus be very general. For example, “Residues” corresponds to the NSL expression “node.type residue”, and “Ions” corresponds to the NSL expression “node.type atom and not (node.type atom linking node.type atom)”. The image below shows the selection filter box.
See how the rectangle selection editor operates depending on the active selection filter, when working with PDB entry 2AZ8. First, using the “Atoms and bonds” filter makes it possible to select atoms and bonds individually:
The “Residues” filter, as the name indicates, selects entire residue nodes:
while the “Side chains” filter selects side chain nodes:
While the selection filters above only match one node type, ligand atoms may be found using the “Ligands” selection filter, which corresponds to a more complex NSL expression (“a.het and not (n.t a and not (n.t a l n.t a)) and not a.w”, i.e. heteroatoms that are not ions and not waters):
Of course, using the rectangle selection editor is not necessary. The “Select all” command (“Selection / Select all”, Ctrl / Command + A) now selects all nodes in the document that match the active selection filter:
The “Select all” command is even more interesting when the active selection filter depends on the selection itself. Here is what happens when repeatedly triggering “Select all” while the “Atoms within 5 A of selection” filter is active:
Selection filters can be customized from the new Find interface.
The new Find interface (activate from the menu “Selection / Find” or with the shortcut Ctrl / Command + F) makes it easy to generate complex Node Specification Language (NSL) expressions. Each widget suggests examples of NSL expressions, and selection filters (see above) can be retrieved and customized.
The example below shows the user first selecting hydrogen atoms, then hydrogen atoms within 4 Angstrom of oxygen atoms:
Of course, once the NSL syntax is acquired, it may be faster to directly type in the selection string:
Updated selection editors
Selection editors (point selection – shortcut S, rectangle selection – shortcut R, and lasso selection – shortcut L) can now directly be used to move objects, and the displacer editor is thus, ahem, displaced. When using these three selection editors, the keyboard may also be used to move the selection: pressing the arrow keys rotates the selection in increments of 15 degrees, and pressing the arrow keys while holding the Ctrl / Command key translates the selection in increments of 1 Angstrom. The example below shows the rectangle selection editor in action, when the active selection filter is “Structural models”.
Molecules may now be rendered with a depth-of-field effect (blurred distant objects). Activate and configure in Preferences.
Screen-space ambient occlusion
This new effect improves the perception of depth in large molecules (activate and configure in Preferences).
There are now two ways to improve the rendering of edges in the viewport: multi-sampling and Fast Approximate Anti-Aliasing (FXAA). Both may be activated and configured from Preferences.
The font for labels can now be customized from Preferences.
The viewport can now be captured and saved to the disk (“Visualization / Capture viewport”, F10). Go to Preferences to configure captures.
Source the research featured in SAMSON Elements
SAMSON Elements may now reference the research on which they’re based. When available, click the question mark on the window title bar to get citation information.
Open and save
The Open and Save dialogs have been merged with the Import and Export dialogs. They can now remember favorite locations.
Upgraded SAMSON file formats
The SAMSON file formats (.sam and .samx) may now manage version numbers of SAMSON and SAMSON Elements, in order to enhance backward compatibility. This means it should be easier to share SAMSON documents between different versions of SAMSON.
Stay tuned for upcoming posts about new SAMSON Elements. If you have comments or questions, please let us know below. Or, even better, join us in Lyon from June 19 to June 23 for SAMSON School 2017!