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Calculate reaction buffer recipes accounting for protein stock contributions. Use when the user asks about designing reaction buffers, calculating buffer volumes, compensation buffers, or setting up biochemistry experiments with proteins.
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| name | reactor |
| description | Calculate reaction buffer recipes accounting for protein stock contributions. Use when the user asks about designing reaction buffers, calculating buffer volumes, compensation buffers, or setting up biochemistry experiments with proteins. |
| allowed-tools | Bash(reactor_cli:*) |
A CLI tool for calculating reaction buffer recipes that account for buffer components contributed by protein stocks.
scripts/reactor_cli.py
# List available presets
python3 scripts/reactor_cli.py --list-presets
# List predefined stock concentrations
python3 scripts/reactor_cli.py --list-stocks
# Calculate using presets
python3 scripts/reactor_cli.py \
--protein-preset kinase_panel \
--buffer-preset kinase_assay \
--volume 100
# Calculate with direct specifications (concentration)
python3 scripts/reactor_cli.py \
--protein "CDK2:50nM:stock=10uM:buffer=HEPES/20mM,NaCl/150mM" \
--buffer "HEPES:1M->25mM" \
--buffer "NaCl:5M->100mM" \
--volume 100
# Calculate using pmol amounts (auto-converted to concentration)
python3 scripts/reactor_cli.py \
--protein "PolII:70pmol:stock=5.17uM:buffer=HEPES/20mM,NaCl/150mM" \
--buffer "HEPES:1M->20mM" \
--volume 100
# Calculate using molar ratios with reference
python3 scripts/reactor_cli.py \
--reference 70pmol \
--protein "PolII:1x:stock=5.17uM:buffer=HEPES/20mM" \
--protein "DSIF:1.5x:stock=50.8uM:buffer=HEPES/20mM" \
--buffer "HEPES:1M->20mM" \
--volume 100
# Use compensation buffer mode (creates concentrated buffer)
python3 scripts/reactor_cli.py \
--protein "MyProtein:100nM:stock=5uM:buffer=HEPES/20mM,NaCl/300mM" \
--buffer "HEPES:1M->25mM" \
--buffer "NaCl:5M->150mM" \
--volume 50 \
--mode compensation \
--fold 10
# Output as JSON
python3 scripts/reactor_cli.py \
--protein-preset kinase_panel \
--buffer-preset storage \
--volume 100 \
--json
Direct Mode (default): Calculates exact volumes of each buffer component to add, accounting for contributions from protein stocks.
Compensation Mode: Creates a concentrated buffer (e.g., 10X) that compensates for buffer components in protein stocks. Useful for preparing batch buffers.
"Name:Amount:stock=StockConc[:buffer=Component/Conc,Component/Conc,...]"
Amount can be specified as:
50nM, 1uM, 100mM70pmol, 100fmol, 1nmol (auto-converted to concentration based on volume)1.5x, 2x (requires --reference flag)Examples:
"CDK2:50nM:stock=10uM" - Simple protein without buffer info"CDK2:50nM:stock=10uM:buffer=HEPES/20mM,NaCl/150mM" - Protein with storage buffer components"PolII:70pmol:stock=5.17uM:buffer=HEPES/20mM" - Using absolute pmol amount"DSIF:1.5x:stock=50.8uM:buffer=HEPES/20mM" - Using molar ratio (with --reference 70pmol)"Name:StockConc->FinalConc"
Examples:
"HEPES:1M->25mM" - HEPES from 1M stock to 25mM final"NaCl:5M->150mM" - NaCl from 5M stock to 150mM final"Glycerol:100%->10%" - Glycerol from 100% to 10% finalProtein Presets (built-in):
kinase_panel - CDK2 and MEK1 for kinase assayspurification_stocks - His-tagged protein and TEV proteasereconstitution - Nucleosome reconstitutionpolii_elongation_complex - Pol II elongation complex (PolII, DSIF, IWS1, ELOF1, SPT6, PAF1c, P-TEFb, CSB, DNA-RNA, ntDNA)Buffer Presets (built-in):
lysis - Cell lysis buffer (50mM HEPES, 300mM NaCl, 1mM TCEP, 5% glycerol)gel_filtration - SEC buffer (25mM Tris, 150mM NaCl, 1mM EDTA, 10% glycerol)storage - Protein storage buffer (20mM HEPES, 150mM NaCl, 0.5mM TCEP, 10% glycerol)kinase_assay - Kinase reaction buffer (25mM HEPES, 100mM NaCl, 10mM MgCl2, 1mM DTT, 1mM ATP)cryo_em - Cryo-EM buffer (20mM HEPES, 150mM NaCl, 1mM TCEP)elongation_buffer - Elongation assay buffer (20mM HEPES, 75mM NaCl, 10% glycerol, 1mM TCEP, 1mM ATP, 3mM MgCl2)Presets can be loaded from external YAML or JSON files using --presets-file. Default locations searched:
~/.config/reactor/presets.yamlCommon laboratory stock concentrations are predefined:
--list-stocks to see all)--reference)