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Assemble and purify macromolecular complexes for structural biology. Use when the user asks about gel filtration, complex assembly, SEC purification, elongation complexes, calculating stoichiometry, or interpreting A260/A280 ratios.
用 Codex 或 Claude 帮你安装 复制这段 Prompt，粘贴到 Codex、Claude 或其他助手里，让它检查 Skill 页面并帮你完成安装。
基于 SOC 职业分类
Predict optimal construct boundaries for protein expression. Use when the user asks about domain boundaries, construct design, truncations, which region of a protein to express, or identifying disordered regions.
Manage lab notebook entries, registry items (plasmids, proteins, etc.), templates, widgets, and audit logs via the Labbook service. Use when creating or viewing lab notebook entries, managing the sample registry, or documenting experiments.
Verify open reading frames (ORFs) in plasmid sequences. Use when the user asks about verifying protein coding sequences, checking if an ORF is present in a plasmid, finding where a protein is encoded, or doing six-frame translation analysis.
Fetch sequencing data from Plasmidsaurus. Use when the user asks about listing sequencing orders, downloading sequencing results, checking order status, or retrieving plasmid sequences from Plasmidsaurus.
Design PCR primers for molecular cloning. Use when the user asks about designing primers, LIC cloning primers, sequencing primers, Gibson assembly primers, or working with NCBI accession codes for cloning.
Calculate protein parameters (MW, pI, extinction coefficient) and generate purification recommendations. Use when the user asks about protein properties, molecular weight, isoelectric point, extinction coefficients, or purification strategies.
| name | complex-formation |
| description | Assemble and purify macromolecular complexes for structural biology. Use when the user asks about gel filtration, complex assembly, SEC purification, elongation complexes, calculating stoichiometry, or interpreting A260/A280 ratios. |
| allowed-tools | Bash(complex_cli:*) |
Guidelines for assembling and purifying macromolecular complexes for structural biology.
| Parameter | Value |
|---|---|
| Column | Superose 6 Increase 3.2/300 |
| System | ÄKTA micro |
| Fraction size | 0.05 mL (50 µL) |
| Void volume | B6 |
| Complex | Expected Fractions | Notes |
|---|---|---|
| Large EC* (full elongation complex) | B4-B5 | DSIF, SPT6, PAF1c, etc. |
| EC* + nucleosome | B5-B6 | May approach void |
| Minimal EC (Pol II + DSIF) | B5-C3 | Intermediate |
| Pol II only | C4-C6 | ~500 kDa reference |
Rule: If complex elutes earlier than expected → possible aggregation. If later → incomplete assembly or dissociation.
| Complex Type | Expected Ratio | Interpretation |
|---|---|---|
| EC* on linear DNA | A280 > A260 | Protein dominates signal |
| Nucleosome-containing | A260 >> A280 | Nucleosomal DNA dominates |
Red flags:
| Application | Target Range | Minimum |
|---|---|---|
| Cryo-EM grids | 100-200 nM | 60 nM |
| Transcription elongation assays | 100-200 nM | 60 nM |
Below 60 nM: Not usable — concentration too low for downstream applications.
complex_cli.py with appropriate preset# List available presets
python3 scripts/complex_cli.py list
# Calculate recipe for EC*
python3 scripts/complex_cli.py ec_star --pol2 5.2uM --volume 100
# Calculate TC-NER complex
python3 scripts/complex_cli.py tc_ner --pol2 5.2uM --volume 100
| Problem | Possible Cause | Solution |
|---|---|---|
| Elutes at void (B6) | Aggregation | Reduce concentration, add salt, check buffer |
| Elutes later than expected | Incomplete assembly | Check component activity, increase incubation |
| Missing bands on gel | Component limiting | Verify stock concentrations, check stoichiometry |
| Extra bands on gel | Contamination/degradation | Check protein quality, use fresh stocks |
| Low A280 signal | Low yield | Scale up input, optimize assembly conditions |
Column calibration is empirical — based on previous runs with known complexes. No formal MW standards are used; positions are learned from experience.
Last updated: 2026-01-17