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What's new in SAMSON 2024 - Modeling#

This is Part III of What's new in SAMSON 2024, the release notes for SAMSON 2024.

New selection commands#

SAMSON 2024 introduces new selection commands (for example to select polar hydrogens, etc.). All commands can be found in the Select menu:

New selection commands in SAMSON

New selection modifiers#

As seen in the image above, the behavior of selection commands and selection modifiers is changed in SAMSON 2024:

  • By default, clicking on a selection command empties the current selection and creates a new selection.
  • Holding Ctrl / Cmd while clicking on the command adds to the current selection.
  • Holding Alt / Option while clicking on the command removes from the current selection.
  • Holding Shift while clicking on the command intersects with the current selection.

Updates to the Node Specification Language#

SAMSON has a very powerful Node Specification Language (NSL) to specify selections of nodes. In SAMSON 2024, the NSL syntax is significantly expanded :

  • Nodes categories: nodes can now be matched by categories. For example, n.c lig matches all ligands, n.c rec selects all receptors and n.c dna selects DNA.
  • Wildcard matches: nodes can now be matched by name using wildcard (*). For example, AL* matches all nodes whose name begins with AL.
  • Lists and ranges: where relevant (e.g., residue id, chain id, atom serial number, atom formal charge, etc.), nodes can now be matched by specifying lists or ranges. For example, r.id 1, 5:10, 12 matches residues whose id is either 1, 5, 6, 7, 8, 9, 10 or 12.
  • Mathematical expressions can now be part of NSL expressions. For example, r.id 3*4:5*4 matches residues 12 to 20.
  • New node attributes are available:
    • For chains: chain.formalCharge, chain.numberOfAtoms, chain.numberOfCoarseGrainedAtoms, chain.numberOfResidues, chain.numberOfStructuralGroups
    • For residues: residue.dna, residue.rna, residue.formalCharge, residue.numberOfAtoms, residue.numberOfCoarseGrainedAtoms
    • For structural groups: structuralGroup.formalCharge, structuralGroup.numberOfAtoms, structuralGroup.numberOfCoarseGrainedAtoms
    • For atoms: atom.polarHydrogen, atom.nonPolarHydrogen, atom.atomicNumber, atom.covalentRadius, atom.vanDerWaalsRadius, atom.mass, atom.electronegativity
  • Boolean attributes do not require using == or != anymore. For example atom.fixed false matches all mobile atoms.

Construction#

The Add editor (shortcut A) now automatically chooses where atoms and bonds are located in a structure hierarchy. For example, when adding a methyl group to a tyrosine side chain, the added atoms are placed in the same side chain:

Add editor: automatically place atoms into the structural hierarchy

The Local Move editor (shortcut M) now makes it easier to edit dihedral angles: click on the half of the bond corresponding to the fragment that you want to rotate, and edit the angle using the widget that appears:

Edit dihedral angle using the Local Move editor

The Twister editor (shortcut T) now makes it straightforward to create handles based on selections and twist any structures:

Twister editor

Next#

Go to Part IV about Coding.