A molecular structure can contain several chains, and they are not always equally relevant to the question at hand. One may be the long polymer you want to inspect; another may be a shorter chain or a chain with multiple segments. Clicking through the structure and checking each one manually can turn a simple filtering task into a distraction.
In SAMSON, the Node Specification Language (NSL) lets you describe what to find. For chain-level searches, the chain attribute space has the short prefix c. A useful starting point is to choose the property that best expresses your intent: chain ID, residue count, segment count, or structural-group count.
Start with the question, not the query
If you know which chain IDs you want to inspect, use the chain ID attribute. For example, c.id 1 matches chain ID 1. To match IDs from 2 through 4, as well as ID 6, use c.id 2:4, 6. This is handy when you have already identified candidate IDs and want to refer to them directly.
If chain length is what matters, search by residue count instead. c.nr > 100 matches chains with more than 100 residues, while c.nr 100:120 matches chains in the documented 100–120 range. This can help you narrow a large structure to longer chains without counting residues by hand.
For a structural organization check, try c.ns > 2 to find chains with more than two segments, or c.nsg > 10 to find chains with more than ten structural groups. These are different measures: use the one that corresponds to the organization you want to examine rather than treating the counts as interchangeable.
A practical chain-first routine
- Write down the question. Are you looking for a particular chain ID, a chain above a size threshold, or one with a particular segment structure?
- Choose the matching attribute. Use
c.idfor IDs,c.nrfor residues,c.nsfor segments, andc.nsgfor structural groups. - Try a focused expression. For example,
c.nr > 100is easier to interpret than a search based on a property that only indirectly reflects chain length. - Refine using what you know. Chain names are inherited from the node attribute space, so expressions such as
c.n "A"orc.n "L*"can be useful when the chain name is the relevant clue.
Thinking in terms of chain-level attributes is especially useful when the task is to narrow the structure before inspecting details. It keeps the search aligned with the unit you care about: a chain, rather than an individual atom or residue. It also makes the intent of a query easier to revisit later. A short expression like c.nr > 100 clearly says what criterion you used.
Know what the prefix means
The c prefix identifies the chain attribute space, which matches chain nodes. Chain attributes also inherit properties from the broader node and structural-group attribute spaces. For example, c.v refers to visibility, while c.fc refers to formal charge. For name matching, values are written as quoted strings; for numeric attributes, the examples use comparisons or ranges.
One small detail can prevent confusion: the chain ID attribute is documented as accepting integers. If you are working from an external file or notes that use letter labels, check how those chains are represented in the SAMSON structure before assuming the label can be entered as an ID. The inherited name attribute is a separate option for matching chain names.
For the complete list of inherited and chain-specific attributes, examples, and details, see the SAMSON chain attributes reference.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.