'cleaning protocol',
sample_prep_method='Plates Clean.setup', # thorough cleaning
itc_method='water5inj.inj',
analysis_method='Control',
experimental_conditions=dict(target_temperature=25,
equilibration_time=60,
stir_rate=1000,
reference_power=5),
injections=5 *
[dict(volume_inj=7.5, duration_inj=15, spacing=150, filter_period=5)],
)
# Define ITC Experiment.
# use specified protocol by default
itc_experiment_set = ITCExperimentSet(
name='Bovine carbonic anhydrase (CAII) experiments')
# Add available plates for experiments.
destination_plate = Labware(RackLabel='DestinationPlate', RackType='ITC Plate')
itc_experiment_set.addDestinationPlate(destination_plate)
nreplicates = 1 # number of replicates of each experiment
# Add cleaning experiment.
name = 'initial cleaning water titration'
itc_experiment_set.addExperiment(
ITCExperiment(name=name,
syringe_source=water_trough,
cell_source=water_trough,
protocol=cleaning_protocol,
cell_volume=cell_volume))
)
# Protocol for cleaning protocol
cleaning_protocol = ITCProtocol(
'cleaning protocol',
sample_prep_method='Plates Clean.setup',
itc_method='water5inj.inj',
analysis_method='Control',
experimental_conditions=dict(target_temperature=25, equilibration_time=60, stir_rate=1000, reference_power=5),
injections=5 * [dict(volume_inj=7.5, duration_inj=15, spacing=150, filter_period=5)],
)
# Define ITC Experiment.
# use specified protocol by default
itc_experiment_set = ITCExperimentSet(name='SAMPL4-CB7 host-guest experiments')
# Add available plates for experiments.
itc_experiment_set.addDestinationPlate(
Labware(
RackLabel='DestinationPlate',
RackType='ITC Plate'))
itc_experiment_set.addDestinationPlate(
Labware(
RackLabel='DestinationPlate2',
RackType='ITC Plate'))
nreplicates = 1 # number of replicates of each experiment
# Add cleaning experiment.
name = 'initial cleaning water titration'
itc_experiment_set.addExperiment(
binding_protocol = ITCProtocol(
'1:1 binding protocol',
sample_prep_method='Plates Standard.setup',
itc_method='Chodera_HSA.inj', # TODO Define new protocol with more injections?
analysis_method='Onesite') # TODO better default analysis?
# Protocol for cleaning protocol
binding_cleaning_protocol = ITCProtocol(
'cleaning protocol',
sample_prep_method='Plates Clean.setup',
itc_method='Chodera_HSA.inj',
analysis_method='Onesite')
# Define ITC Experiment.
# use specified protocol by default
itc_experiment_set = ITCExperimentSet(name='Human Serum Albumin experiments')
# Add available plates for experiments.
itc_experiment_set.addDestinationPlate(
Labware(
RackLabel='DestinationPlate',
RackType='ITC Plate'))
itc_experiment_set.addDestinationPlate(
Labware(
RackLabel='DestinationPlate2',
RackType='ITC Plate'))
nreplicates = 1 # number of replicates of each experiment
# Add water control titrations.
for replicate in range(1):
buffer_masses = {'Compound 10': 10.065 * ureg.gram}
compound_masses = {'Compound 10': 15.05 * ureg.milligram}
ligand_solutions = list()
for (index, ligand) in enumerate(ligands):
ligand_solution = SimpleSolution(
compound=ligand,
compound_mass=compound_masses[ligand.name],
solvent=buffer,
solvent_mass=buffer_masses[ligand.name],
location=PipettingLocation(source_plate.RackLabel,
source_plate.RackType, index + 1))
ligand_solutions.append(ligand_solution)
# For convenience, report concentrations
print('STOCK SOLUTION CONCENTRATIONS:')
location = ITCExperimentSet.human_readable(receptor_solution.location)
print(
f"{receptor_solution.name:20} in {location:32} : {receptor_solution.compound_mass.to('milligrams')} receptor in {receptor_solution.solvent_mass.to('grams')} solvent : {receptor_solution.concentration.to('millimolar'):30}"
)
for ligand_solution in ligand_solutions:
location = ITCExperimentSet.human_readable(ligand_solution.location)
print(
f"{ligand_solution.name:20} in {location:32} : {ligand_solution.compound_mass.to('milligrams')} compound in {ligand_solution.solvent_mass.to('grams')} solvent : {ligand_solution.concentration.to('millimolar'):30}"
)
print('')
# Define ITC protocol.
# Receptor cell concentrations to evaluate
#cell_concentrations = [0.010 * ureg.millimolar, 0.020 * ureg.millimolar, 0.030 * ureg.millimolar]
#cell_concentrations = [0.020 * ureg.millimolar]
'cleaning protocol',
sample_prep_method='Plates Clean.setup',
itc_method='water5inj.inj',
analysis_method='Control',
experimental_conditions=dict(target_temperature=25,
equilibration_time=60,
stir_rate=1000,
reference_power=5),
injections=5 *
[dict(volume_inj=7.5, duration_inj=15, spacing=150, filter_period=5)],
)
# Define ITC Experiment.
# use specified protocol by default
itc_experiment_set = ITCExperimentSet(name='HDR')
# Add available plates for experiments.
itc_experiment_set.addDestinationPlate(
Labware(RackLabel='DestinationPlate', RackType='ITC Plate'))
itc_experiment_set.addDestinationPlate(
Labware(RackLabel='DestinationPlate2', RackType='ITC Plate'))
nreplicates = 1 # number of replicates of each experiment
# Add cleaning experiment.
name = 'initial cleaning water titration'
itc_experiment_set.addExperiment(
ITCExperiment(
name=name,
syringe_source=water_trough,
cell_source=water_trough,
cleaning_protocol = ITCProtocol(
'cleaning protocol',
sample_prep_method='Plates Clean.setup',
itc_method='ChoderaWaterWater5.inj',
analysis_method='Onesite',
experimental_conditions=dict(target_temperature=25, equilibration_time=60, stir_rate=1000, reference_power=5),
injections=5 * [
dict(volume_inj=7.5, duration_inj=15, spacing=150, filter_period=5)],
)
# Define ITC Experiment.
# use specified protocol by default
itc_experiment_set = ITCExperimentSet(name='Human Serum Albumin experiments')
# Add available plates for experiments.
itc_experiment_set.addDestinationPlate(
Labware(
RackLabel='DestinationPlate',
RackType='ITC Plate'))
itc_experiment_set.addDestinationPlate(
Labware(
RackLabel='DestinationPlate2',
RackType='ITC Plate'))
nreplicates = 1 # number of replicates of each experiment
# # Initial cleaning is skipped.
# name = 'initial cleaning water titration'