Jean by Melad Labs

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. A Scorpion is a primer carrying a stem-loop probe on a non-amplifiable blocker (Whitcombe 1999), and it reports by the loop finding its target and pulling the stem apart - so the design question is a RELATION between those two structures, not a property of either. Returns both temperatures, their difference, the stem's GC, and a verdict against WHATEVER margin you pass. It does not apply a margin of its own authority: the widely-quoted 5-10 °C figure comes from one design tool's tech note and has no primary citation, so the default is labelled as that rule of thumb and every result says which margin produced its verdict.

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

A4.4/5.0

Behavior5/5

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

Annotations already declare readOnlyHint and openWorldHint=false, but the description adds substantial context: what the result contains, that the verdict is computed against a caller-supplied margin, and a candid disclosure that the popular 5-10 °C rule has no primary citation and is labelled as a rule of thumb rather than enforced. That is exactly the kind of provenance and authority caveat an agent cannot get from structured fields.

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

Conciseness4/5

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

Front-loaded with what is computed and why the relation matters, which is the right ordering. It is dense but earns most sentences; the closing restatement of the margin caveat partially duplicates the clause earlier in the same paragraph, costing a bit of tightness.

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

Completeness5/5

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

With an output schema present and 100% schema coverage, the description needn't explain return values, yet it still names them (both Tms, difference, stem GC, verdict). The chemistry background and the margin provenance are exactly the extra context this tool needs, so nothing an agent requires to call it correctly is missing.

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 margin parameter's schema text already carries the 'rule of thumb, not primary literature' caveat, so the description largely restates rather than extends parameter meaning. It does reinforce that the probe string must be the whole element and that target is the other temperature, but these are already documented in the schema.

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

Purpose5/5

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

States a concrete verb and resource (check a Scorpion probe's stem) and defines the computation precisely: two melting temperatures, their difference, the stem GC, and a verdict. It also distinguishes itself conceptually from single-Tm siblings by insisting the design question is 'a RELATION between those two structures, not a property of either', which is exactly the boundary against melting_temperature.

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

Usage Guidelines4/5

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

It gives clear context for when this tool applies: Scorpion probe design, where the loop-target duplex must open the stem. It never names an alternative sibling or states an explicit when-not condition, so the agent must infer the boundary with melting_temperature / scan_oligo_structure rather than being routed.

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

All Jean by Melad Labs tools Inspect

Try in Browser

One endpoint for every MCP toolRayrun runs every MCP server behind one URL and holds the credentials. Each call is decided per client, tool, and argument, then recorded.ray.runAd

Glama MCP Gateway

Add one secure layer between your agents and this server.

Resources

Need Help?