CC structure-analysis
Handles protein structure files and geometric criteria so that residue counts, contacts, hydrogen bonds and interfaces are reproducible, covering PDB versus mmCIF, author versus label chains and numbering, HETATM, water and ligand policy, alternate locations, insertion codes, biological assemblies versus the asymmetric unit, hydrogen-bond distance and angle cutoffs, interface definitions by distance or buried surface area, and the Biopython, MDAnalysis, gemmi, PyMOL and ChimeraX calls that implement them. Use whenever a task reads a structure file and reports anything derived from atom coordinates; use biopython for sequence work and molecular-docking or structure-prediction skills for generating structures.
Handles protein structure files and geometric criteria so that residue counts, contacts, hydrogen bonds and interfaces are reproducible, covering PDB versus…
As a process C 57/100 · Has gaps — weak spots: result and completion, inputs and preconditions, failures and branches
What is at stake
Medium-severity findings: the skill is probably honest, but read what alarmed the scanner.
Below is the worst case for this category. The finding here is medium: the guard saw a sign, not a proof.
The skill asks for more than the task needs: broad tool access, credential environment variables, binaries. Every extra permission widens the damage from a mistake or a compromise.
Narrow allowed-tools and the variable list to the minimum; replace binaries with readable sources or scripts.
How to improve
- Your own cases (evals/evals.json, 4–6 real requests with expected answers): the full check would then run those instead of a model-drafted suite.
- A spec.yaml with trigger phrases and assertions — a behaviour contract for CI; `skilltest init` writes a template.
Guard findings · 1
✓ No critical or high findings
Medium and low: 1
-
medium Broad scope
meta-broad-allowed-toolsSKILL.md:1Broad tool permissions pre-approved: Bashallowed-tools: Read Bash python
Files scanned: 1. Evidence is masked. Grey chips explain why severity was lowered.
Against the Agent Skills spec
- note
frontmatter-keyunknown frontmatter key "summary" - note
edit-residuethe text marks something as outdated (lines 11, 91): check that old rules are not kept next to new ones — the full check reads the text for contradictions
Process rating: all ten parameters 57/100
- 0Result and completion. Does not say what the result is
- 0Inputs and preconditions. Does not say what the process needs to start
- 0Failures and branches. Linear process with no failure handling
- 0Progress reporting. Says nothing while it works
- 30Running it twice. 7 mutating operations with no state check
- 70When it triggers. States when to use, but not when not to
- 100Tools and files. Tools declared in frontmatter
- 100Steps. 24 steps
- 100Consistency. Name and required fields are in place
- 100Execution cost. Instruction body is 1675 tokens
Everything here is measured from the skill text rather than judged by a model, so the numbers are checkable. A parameter weighs more when it is a more common reason for the process to stall.
Quality signals
- +5Description has no quoted example phrases that should trigger the skill
- +4Description does not say when NOT to use the skill (false activations)
- +3Output format is not stated: the model decides each time
- +4No input/output examples
- +2Single-language instructions
- +3Description length 717: enough signal without eating the budget
- +4Structure: 5 headings
- +3Step-by-step instructions: 24 items
- +1License stated
Quality base 70; lint remarks subtract, signals add up to 100. Result: 80.