Jean — Molecular Biology & Genomics

check_scorpion_stem

Read-only

A Scorpion probe's two melting temperatures, side by side: the stem-loop's own hairpin and the duplex the loop makes with its target on the amplicon.

Input Schema

Name	Required	Description
`probe`	Yes	the whole probe element, 5' stem arm + loop + 3' stem arm. The element is what folds, so it is what the structure engine is given - the loop alone would compute a hairpin the molecule does not have.
`_files`	No	The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
`margin`	No	how many °C the stem Tm must exceed the loop-target Tm for the verdict to pass. Yours to set: the 5-10 °C rule of thumb this defaults to the floor of is a design tool's, not a measured value from the primary literature. In °C.
`target`	Yes	the loop's target on the amplicon, 5'->3'. This is the OTHER temperature: a Scorpion opens because the loop finds this, so it is the loop-target duplex that has to be stable, not the loop's own self-structure.
`_subject`	No	The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
`conditions`	No	salt, magnesium, dNTP and oligo concentrations plus the salt-correction method the stem Tm is measured in. Left unset it is filled from your reaction-conditions settings, and falls back to primer3's defaults when there are none. Advanced.
`stem_length`	No	how many bases of the 5' end form the stem arm. Reported back rather than guessed. The two vendors disagree on the range - LGC Biosearch, who sell Scorpions, publish 5-7 nt and PremierBiosoft's design tool says 6-7 - so neither is enforced. In nt.

Output Schema

Name	Required	Description
`notes`	Yes	why a temperature is missing, in the words the panel shows. Empty when both were computed
`stemTm`	Yes	melting temperature of the probe element's own hairpin, °C - null when no stem forms
`probeTm`	Yes	melting temperature of the loop-target duplex, °C
`difference`	Yes	stemTm - probeTm, the quantity the design rule is about
`clearsMargin`	Yes	whether the difference clears the margin GIVEN - null when either temperature could not be computed
`marginSource`	Yes	where the margin came from, carried with the verdict so an unsourced rule of thumb is never mistaken for a measurement
`stemGcPercent`	Yes	GC of the 5' stem arm - both vendors ask for a GC-rich stem

Schema Changelog

Changes observed during successful MCP inspections.

Changed3 schema fields changedOct 25, 2026
- addedOutput schema / properties / difference / x-unit
```
Added value: +"°C"
```
- addedOutput schema / properties / probeTm / x-unit
```
Added value: +"°C"
```
- addedOutput schema / properties / stemTm / x-unit
```
Added value: +"°C"
```

Changed1 schema field changedOct 23, 2026

addedInput schema / properties / conditions / properties / selfcomp

Added value: +{
+  "description": "both strands are one self-complementary oligo (the concentration term becomes dnac1 rather than dnac1 − dnac2/2).",
+  "type": "boolean"
+}

First observedOct 20, 2026

TDQS

B3.4/5.0

Behavior3/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare readOnlyHint=true, destructiveHint=false and openWorldHint=false, so the safety profile is fully covered and the description need only add computation context. It does add the framing that two distinct Tms are produced and which molecules each belongs to, but says nothing about the pass/fail verdict the margin parameter implies, nor about sensitivity to the conditions block, which the schema alone flags as 'advanced'.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

A single sentence, front-loaded with the resource and the deliverable, with zero filler. Nothing in it is redundant or misplaced.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

An output schema exists, annotations carry the safety profile, and every parameter is individually documented, so the description does not need to explain return values or field syntax. What is missing is any statement of what the tool concludes (the stem-Tm-exceeds-loop-Tm verdict governed by margin), which is the reason an agent would call it — a small but real gap for a tool with a decision-oriented output.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100% and the nested parameters (conditions, additives, _subject) are documented in detail, so the schema does the heavy lifting. The description contributes a little: it clarifies that the 'target' is the loop's binding site on the amplicon rather than a general template. Baseline 3 is appropriate; it neither duplicates nor materially extends the per-parameter text.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The sentence names a concrete object (a Scorpion probe) and a concrete output (two melting temperatures reported side by side), specifying which two: the stem-loop hairpin and the loop-target duplex. That is enough for an agent to tell it apart from generic siblings like melting_temperature or fold_rna. It stops short of 5 because it never states the action as a verb (compute/compare/check) nor names the sibling it supersedes.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

There is no when-to-use or when-not-to-use guidance, no prerequisite stated, and no alternative tool named. The only scoping is implicit in the words 'Scorpion probe'. Nothing tells the agent to reach for this over melting_temperature when checking a Scorpion design, or to avoid it for ordinary primer pairs.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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