In molecular modeling, it’s common to need specific subsets of atoms for tasks like analysis, visualization, or simulation. For example, you might want to display only the oxygen atoms in a protein, exclude hydrogens, or select planar aromatic carbons. Performing such queries manually can be time-consuming and error-prone, especially for large molecular systems.
This is where the Node Specification Language (NSL) in SAMSON becomes a valuable tool. NSL allows you to search atoms based on well-defined attributes. While NSL covers a wide range of features, this blog post will focus on atom attributes that help select atoms based on their core chemical identity and bonding behavior.
Commonly Used Atom Filters You Should Know
Here’s a breakdown of some of the most practical attributes you can use immediately to streamline your selection workflows:
1. Select by Element or Symbol
If you want to highlight or work only with atoms of certain elements:
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a.e Oxygen |
or, using element symbols:
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a.s O a.s H, C, N |
2. Select Atoms with Specific Aromaticity
To find aromatic atoms:
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a.ar |
To find aromatic carbon atoms:
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a.s C and a.ar |
3. Planar Atoms
Planar atoms (those in a plane with their bonded neighbors) can be selected using:
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a.pl |
This is useful for identifying sp2 centers or conformational constraint regions.
4. Geometry Filters
If you’ve assigned geometry to atoms, this becomes a powerful filter:
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a.g tet</code> → tetrahedral a.g l</code> → linear a.g o</code> → octahedral |
To find atoms with either octahedral or dodecahedral geometry:
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a.g o, d |
Geometry attributes must be computed first in SAMSON.
5. Selection by Atomic Number
Sometimes you might want to select atoms purely by their atomic number:
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a.at 6</code> → carbon (atomic number 6) a.at 6,8</code> → carbon and oxygen |
6. Built-in Chemical Categories
Looking for specific families of elements? You can use built-in categories too:
a.hal→ Halogens (F, Cl, Br, I, At)a.met→ Metalsa.alkali→ Alkali metalsa.nobleGas→ Noble gases
Combining Filters for Advanced Queries
NSL lets you use logical operators to combine filters:
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a.s O and a.w</code> → Oxygen atoms flagged as water a.s C and a.ar and a.pl</code> → Planar aromatic carbon atoms a.e Carbon and not a.ar</code> → Non-aromatic carbon atoms |
Tips for Usage
- If you’re unsure about attribute names or syntax, use the NSL panel in SAMSON, which often auto-completes inputs.
- Geometry and hybridization may require prior assignment—make sure your system is annotated appropriately.
- Use short names (
a.s,a.at, etc.) to keep your expressions concise.
Using these filters, modelers can more easily prepare selections for simulation, visualize specific atoms, or apply operations to atom subsets without tedious manual clicking. This can simplify workflows and eliminate errors in large molecular systems.
To see the full list of supported atom attributes and their meanings, visit the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.