When a protein structure contains thousands of atoms, spotting regions that may need inspection can become a tedious search. Low occupancy or a high temperature factor can help flag atoms for review—but either value needs to be interpreted in the context of the structure. In SAMSON, the Node Specification Language (NSL) lets you combine these properties into a reusable selection instead of checking atoms one by one.
Start with a focused filter
For example, this expression selects heavy atoms with a temperature factor above 50 and occupancy below 0.8:
a.heavy and a.tf > 50 and a.oc < 0.8
a.heavy excludes hydrogen atoms. The other two conditions narrow the selection to atoms meeting both thresholds. In NSL, and combines conditions, while comparison operators such as > and < let you specify numeric cutoffs. The corresponding full attribute names are atom.heavy, atom.temperatureFactor, and atom.occupancy.
Keep the selection relevant
A structure may contain water molecules or atoms from multiple chains. Add conditions to narrow the result—for instance, to look only at heavy atoms in chain A and residue numbers 40 through 60:
a.heavy and a.c A and a.resi 40:60
Here, a.c is the short name for chain, and a.resi is the short name for residue sequence number. A range such as 40:60 provides a compact way to include a span of residue numbers. You can combine those conditions with the earlier filter:
a.heavy and a.c A and a.resi 40:60 and a.tf > 50 and a.oc < 0.8
If you want to exclude atoms flagged as water, add not a.w, where a.w is the water attribute:
a.heavy and not a.w and a.tf > 50 and a.oc < 0.8
Treat cutoffs as a starting point
These expressions help you locate atoms for inspection; they do not diagnose why an atom has a particular value. Temperature factors are commonly associated with atomic displacement or disorder in crystallographic structures, but their interpretation depends on the data and context. Occupancy records how fully a site is represented in the structural model. A high temperature factor or low occupancy can be a useful clue, not a verdict about model quality.
The values 50 and 0.8 above are example thresholds, not universal rules. Adjust them to suit the structure and the question you are asking. You can also test a broader filter first, then add chain, residue, element, or water conditions to make the selection more manageable.
Make selection expressions work for you
Short names keep expressions compact, while full attribute names can make them easier to read when you return to them later. For example, a.tf > 50 is equivalent to using the full temperature-factor attribute, and a.oc < 0.8 refers to occupancy. Commas can specify alternative values for attributes such as chain or element; ranges are useful for numeric attributes such as residue sequence number.
The practical benefit is a clear, repeatable way to ask a structural question: which atoms meet these criteria, in this part of the model? Use the result as a focused starting point for visual inspection or further analysis, and record the thresholds you chose so the selection remains understandable.
For the complete list of atom attributes, short names, value types, and examples, see the SAMSON atom attributes reference.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.