Too many conformations? Start by filtering on atom count

When a molecular system contains many conformations, finding the ones worth inspecting can feel like searching a long list one entry at a time. A useful first step is to narrow the list by a simple, objective property: how many atoms each conformation contains. In SAMSON, the Node Specification Language (NSL) provides a dedicated attribute for this.

The key distinction is that conformation is an attribute space for matching conformation nodes. Its short name is co. The atom-count attribute is numberOfAtoms, shortened to nat. Put together, the compact expression is co.nat.

Find conformations above a size threshold

If you want to match conformations containing more than 100 atoms, use:

co.nat > 100

The longer form is conformation.nat > 100. Both express the same criterion: the matched conformation has a number of atoms greater than 100. This is a practical way to separate larger conformations from smaller ones before focusing on a particular size range.

Narrow the search to a range

To match conformations with atom counts between 100 and 200, the documented range expression is:

co.nat 100:200

You can also write conformation.nat 100:200. The colon separates the endpoints of the range. If the exact handling of boundary values matters for your analysis, check the results at the endpoints rather than assuming whether those values are included.

Watch the short-name distinction

One easy mistake is to confuse co.nat with co.n. Here, nat means number of atoms, while n is the inherited name attribute. For example, co.n "A" matches a conformation by name; it does not specify an atom count. Use co.nat when the criterion is size.

The reference table also shows co.n 100:200 beside the atom-count examples. Since the detailed description identifies nat as the number-of-atoms attribute and gives co.nat 100:200 for the range, use the latter form for an atom-count query.

Keep the scope of the query in mind

These expressions match conformations, not individual atoms. That distinction matters when interpreting a result: a match says that the conformation node meets the stated atom-count condition. It is not an instruction to select a subset of atoms within a conformation.

Conformations also inherit node attributes. For instance, co.selected and not co.selected refer to selection state, and co.sf is the short form for selectionFlag. These can help express other node-level criteria, but they are separate from the atom-count test. The selected attribute has no short name in this attribute space, so use co.selected, not co.s.

A small, repeatable workflow

  1. Decide what range of conformation sizes is relevant to the question you are investigating.
  2. Use co.nat > value for a lower-threshold search, or co.nat lower:upper for a range.
  3. Check that the query uses nat, not n, when you mean atom count.
  4. Review the matched conformations and adjust the threshold or range if needed.

This simple filter can make a large set easier to explore without changing the underlying molecular model. It is especially useful as an initial narrowing step; the atom count alone does not describe a conformation’s geometry or tell you whether it is scientifically suitable.

For the complete attribute reference and additional syntax details, see the SAMSON conformation attributes documentation.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.

Comments are closed.