ExperimentPowderXRD

generates a Protocol object for measuring the x-ray diffraction of powder Samples.

Powder X-Ray Diffraction (Powder XRD, PXRD) is a technique that is used to determine crystallographic information about a powder sample. In this technique, X-rays of a known wavelength are collimated onto a powder sample over a range of angles, where at each angle the X-rays are reflected into an X-ray detector. When short- or long-term atomic order exists in the sample, photons can be scattered constructively at certain angles between the X-ray source and detector due to a relationship between the distance between repeating units in the sample and the incident X-ray angle (see Bragg's law). The resulting diffraction patterns (profiles of X-ray scattering intensity over the range of angles) can be used to determine crystallographic information about the distance between repeating units in the sample (and therefore crystal structure), as well as other physicochemical properties such as lattice strain or grain size in poly-crystalline materials.

Experimental Principles

Figure 1.1: Procedural overview of a powder XRD experiment. Step 1: The samples to be analyzed are added to a well plate that is compatible with the XRD instrument. Step 2: The well plate is inserted into an actuating sample holder. The X-ray beam is then transmitted through the sample while the sample is rotated to record the X-ray diffraction pattern (diffractogram). If requested the X-ray detector angle is incremented to collect the diffraction pattern at larger angles. Step 3: After data acquisition is complete, the collected diffractograms are composited and analyzed.

Instrumentation

XtaLAB Synergy-R

Figure 2.1.1: Powder samples are loaded into a 96-well plate, and an X-ray beam is transmitted through each sample from the exit of the X-ray collimator into the X-ray detector on the opposite side of the sample. A fixed position beam stop prevents transmission of X-rays that are not diffracted to the beam detector, protecting the detector from damage that could result from the high flux of radiation. The X-ray detector is rotated about a central axis to collect diffracted X-rays from -50° to 80° 2θ. The sample holder may also rotate the sample ω angle (an ω angle of 0° indicates the sample plate is perpendicular to the X-ray source), increasing the range of the XRD pattern up to 34.5 degrees in total (17.25 degrees in either direction).

Experiment Options

General

Instrument

The diffractometer used for this experiment.

Default Value: Model[Instrument, Diffractometer, XtaLAB Synergy-R]

Pattern Description: An object of type or subtype Model[Instrument, Diffractometer] or Object[Instrument, Diffractometer]

Programmatic Pattern: ObjectP[{Model[Instrument, Diffractometer], Object[Instrument, Diffractometer]}]

TransferType

How samples are to be transferred to the CrystallizationPlate via Slurry or MassTransfer. The model of crystallization plate used is determined by this option.

Figure 3.1: Crystallization plate preparation. Left: When TransferType is Slurry, a suspension of solid (or dissolved solid) is aspirated into wells of the crystallization plate. Afterwards, solvent is removed by evaporation to isolate the solid sample. Right: When TransferType is MassTrasnfer, a finely-ground solid is dispensed to a funnel-shaped well of the crystallzation plate. Solid is tamped into ~0.5 mm diameter capillary at the base of the funnel.

Default Value: Automatic

Pattern Description: Slurry or MassTransfer.

Programmatic Pattern: (Slurry | MassTransfer) | Automatic

X-Ray Parameters

ExposureTime

The length of time the powder sample is exposed to the x-rays for each scan.

Default Value: 0.2 seconds

Pattern Description: Greater than or equal to 0.025 seconds and less than or equal to 1 hour.

Programmatic Pattern: RangeP[0.025*Second, 1*Hour]

Index Matches to: experiment samples

Current

The current used to generate the x-rays in this experiment.

Default Value: 30 milliamperes

Pattern Description: Greater than or equal to 10 milliamperes and less than or equal to 30 milliamperes.

Programmatic Pattern: RangeP[10*Milliampere, 30*Milliampere]

Detector Parameters

DetectorDistance

The distance from the powder sample to the detector.

Default Value: Automatic

Default Calculation: Automatically set from the MinOmegaAngle, MaxOmegaAngle, MinDetectorAngle and MaxDetectorAngle options.

Pattern Description: Greater than or equal to 61 millimeters and less than or equal to 209 millimeters.

Programmatic Pattern: RangeP[61*Millimeter, 209*Millimeter] | Automatic

Index Matches to: experiment samples

DetectorRotation

Determines whether the detector stays in one position or moves through multiple position through the course of a run.

Default Value: Automatic

Default Calculation: Automatically set from the MinOmegaAngle, MaxOmegaAngle, and OmegaAngleRange options.

Pattern Description: Fixed or Sweeping.

Programmatic Pattern: (Fixed | Sweeping) | Automatic

Index Matches to: experiment samples

FixedDetectorAngle

The angle between the X-ray source and the detector held constant through each data recording of a given sample.

Default Value: Automatic

Default Calculation: Automatically set to Null if DetectorRotation-> Sweeping, or to 0 AngularDegree if DetectorRotation-> Fixed.

Pattern Description: Greater than or equal to -50.49 degrees and less than or equal to 81.24 degrees or Null.

Programmatic Pattern: (RangeP[-50.49*AngularDegree, 81.24*AngularDegree] | Automatic) | Null

Index Matches to: experiment samples

MinDetectorAngle

The initial angle between the X-ray source and the detector during the sweeping of detector angle during data recording of a given sample.

Default Value: Automatic

Default Calculation: Automatically set to Null if DetectorRotation -> Fixed, or to an angle based on the DetectorDistance option if DetectorRotation -> Sweeping.

Pattern Description: Greater than or equal to -50.49 degrees and less than or equal to 81.24 degrees or Null.

Programmatic Pattern: (RangeP[-50.49*AngularDegree, 81.24*AngularDegree] | Automatic) | Null

Index Matches to: experiment samples

MaxDetectorAngle

The final angle between the X-ray source and the detector during the sweeping of detector angle during data recording of a given sample.

Default Value: Automatic

Default Calculation: Automatically set to Null if DetectorRotation-> Fixed, or to an angle based on the DetectorDistance option if DetectorRotation-> Sweeping.

Pattern Description: Greater than or equal to -50.49 degrees and less than or equal to 81.24 degrees or Null.

Programmatic Pattern: (RangeP[-50.49*AngularDegree, 81.24*AngularDegree] | Automatic) | Null

Index Matches to: experiment samples

DetectorAngleIncrement

The degree of change in the detector's angle in relation to X-ray source between each set of scans.

Default Value: Automatic

Default Calculation: Automatically set to Null if DetectorRotation -> Fixed, or from the MinDetectorAngle and MaxDetectorAngle options.

Pattern Description: Greater than or equal to 0.1 degrees and less than or equal to 69 degrees or Null.

Programmatic Pattern: (RangeP[0.1*AngularDegree, 69*AngularDegree] | Automatic) | Null

Index Matches to: experiment samples

Sample Handler Parameters

MinOmegaAngle

The angle between the sample and the X-ray source in this run during the first scan of the sample's run if DetectorRotation -> Fixed.

Default Value: Automatic

Default Calculation: Automatically set to Null if DetectorRotation-> Sweeping, or to an angle based on the DetectorDistance, MaxOmegaAngle, and OmegaAngleIncrement options if DetectorRotation-> Fixed.

Pattern Description: Greater than or equal to -17.24 degrees and less than or equal to 17.24 degrees or Null.

Programmatic Pattern: (RangeP[-17.24*AngularDegree, 17.24*AngularDegree] | Automatic) | Null

Index Matches to: experiment samples

MaxOmegaAngle

The angle between the sample and the X-ray source in this run during the last scan of the sample's run if DetectorRotation -> Fixed.

Default Value: Automatic

Default Calculation: Automatically set to Null if DetectorRotation-> Sweeping, or to an angle based on the DetectorDistance, MinOmegaAngle, and OmegaAngleIncrement options if DetectorRotation-> Fixed.

Pattern Description: Greater than or equal to -17.24 degrees and less than or equal to 17.24 degrees or Null.

Programmatic Pattern: (RangeP[-17.24*AngularDegree, 17.24*AngularDegree] | Automatic) | Null

Index Matches to: experiment samples

OmegaAngleIncrement

The degree of change in the sample's angle in relation to X-ray source between each scan. If DetectorRotation -> Sweeping, this rotation occurs for each detector angle as many times as required to reach 2 degrees. Thus, if set to 0.5 degrees, there will be 4 scans per detector angle.

Default Value: Automatic

Default Calculation: Automatically set to 0.5 AngularDegree if DetectorRotation -> Sweeping, or from the MinOmegaAngle and MaxOmegaAngle options.

Pattern Description: Greater than or equal to 0.1 degrees and less than or equal to 2. degrees.

Programmatic Pattern: RangeP[0.1*AngularDegree, 2.*AngularDegree] | Automatic

Index Matches to: experiment samples

Protocol

SpottingVolume

The amount of sample to be spotted on each well of the crystallization plate.

Default Value: Automatic

Default Calculation: Automatically set to 3 Microliter for TransferType -> Slurry.

Pattern Description: Greater than or equal to 1 microliter and less than or equal to 5 microliters or Null.

Programmatic Pattern: (RangeP[1*Microliter, 5*Microliter] | Automatic) | Null

Index Matches to: experiment samples

CrystallizationPlatePreparation

Indicates if the sample loading onto the crystallization plate should occur manually or on a robotic liquid handler.

Default Value: Automatic

Pattern Description: Manual or Robotic.

Programmatic Pattern: PreparationMethodP | Automatic

NumberOfReplicates

The number of times to repeat x-ray diffraction reading on each provided sample. Specifying this option will result in the same sample being aliquoted into multiple wells in the X-ray plate.

Default Value: Null

Pattern Description: Greater than or equal to 2 in increments of 1 or Null.

Programmatic Pattern: GreaterEqualP[2, 1] | Null

ImageXRDPlate

Indicates if the crystallization plate should be imaged after preparing and drying of plates but before loading onto the diffractometer.

Default Value: Automatic

Default Calculation: Automatically set to the template value, or False if no template exists.

Pattern Description: True or False.

Programmatic Pattern: BooleanP | Automatic

Post Experiment

SamplesInStorageCondition

The non-default conditions under which the SamplesIn of this experiment should be stored after the protocol is completed. If left unset, SamplesIn will be stored according to their current StorageCondition.

Default Value: Null

Pattern Description: {AmbientStorage, Refrigerator, Freezer, DeepFreezer, CryogenicStorage, YeastIncubation, YeastShakingIncubation, BacterialIncubation, BacterialShakingIncubation, MammalianIncubation, ViralIncubation, CrystalIncubation, AcceleratedTesting, IntermediateTesting, LongTermTesting, UVVisLightTesting} or Disposal or Null.

Programmatic Pattern: (Alternatives[SampleStorageTypeP | Disposal]) | Null

Index Matches to: experiment samples

SamplesOutStorageCondition

The non-default conditions under which any new samples generated by this experiment should be stored after the protocol is completed. If left unset, the new samples will be stored according to their Models' DefaultStorageCondition.

Default Value: Null

Programmatic Pattern: (Alternatives[SampleStorageTypeP | Disposal]) | Null

Index Matches to: experiment samples

Sample Prep Options

Sample Preparation

PreparatoryUnitOperations

Specifies a sequence of transferring, aliquoting, consolidating, or mixing of new or existing samples before the main experiment. These prepared samples can be used in the main experiment by referencing their defined name. For more information, please reference the documentation for ExperimentSampleManipulation.

Default Value: Null

Pattern Description: List of one or more unit Operation ManualSamplePreparation or RoboticSamplePreparation or unit Operation must match SamplePreparationP entries or Null.

Programmatic Pattern: {((ManualSamplePreparationMethodP | RoboticSamplePreparationMethodP) | SamplePreparationP)..} | Null

PreparatoryPrimitives

Default Value: Null

Pattern Description: List of one or more a primitive with head Define, Transfer, Mix, Aliquot, Consolidation, FillToVolume, Incubate, Filter, Wait, Centrifuge, or Resuspend entries or Null.

Programmatic Pattern: {SampleManipulationP..} | Null

Preparatory Incubation

Incubate

Indicates if the SamplesIn should be incubated at a fixed temperature prior to starting the experiment or any aliquoting. Sample Preparation occurs in the order of Incubation, Centrifugation, Filtration, and then Aliquoting (if specified).

Default Value: Automatic

Default Calculation: Resolves to True if any of the corresponding Incubation options are set. Otherwise, resolves to False.

Pattern Description: True or False.

Programmatic Pattern: BooleanP | Automatic

Index Matches to: experiment samples

IncubationTemperature

Temperature at which the SamplesIn should be incubated for the duration of the IncubationTime prior to starting the experiment.

Default Value: Automatic

Pattern Description: Ambient or greater than or equal to -20 degrees Celsius and less than or equal to 500 degrees Celsius or Null.

Programmatic Pattern: ((Ambient | RangeP[$MinIncubationTemperature, $MaxIncubationTemperature]) | Automatic) | Null

Index Matches to: experiment samples

IncubationTime

Duration for which SamplesIn should be incubated at the IncubationTemperature, prior to starting the experiment.

Default Value: Automatic

Pattern Description: Greater than or equal to 1 minute and less than or equal to 72 hours or Null.

Programmatic Pattern: (RangeP[1*Minute, $MaxExperimentTime] | Automatic) | Null

Index Matches to: experiment samples

Mix

Indicates if this sample should be mixed while incubated, prior to starting the experiment.

Default Value: Automatic

Default Calculation: Automatically resolves to True if any Mix related options are set. Otherwise, resolves to False.

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

Index Matches to: experiment samples

MixType

Indicates the style of motion used to mix the sample, prior to starting the experiment.

Default Value: Automatic

Default Calculation: Automatically resolves based on the container of the sample and the Mix option.

Pattern Description: Roll, Vortex, Sonicate, Pipette, Invert, Stir, Shake, Homogenize, Swirl, Disrupt, or Nutate or Null.

Programmatic Pattern: (MixTypeP | Automatic) | Null

Index Matches to: experiment samples

MixUntilDissolved

Indicates if the mix should be continued up to the MaxIncubationTime or MaxNumberOfMixes (chosen according to the mix Type), in an attempt dissolve any solute. Any mixing/incubation will occur prior to starting the experiment.

Default Value: Automatic

Default Calculation: Automatically resolves to True if MaxIncubationTime or MaxNumberOfMixes is set.

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

Index Matches to: experiment samples

MaxIncubationTime

Maximum duration of time for which the samples will be mixed while incubated in an attempt to dissolve any solute, if the MixUntilDissolved option is chosen. This occurs prior to starting the experiment.

Default Value: Automatic

Default Calculation: Automatically resolves based on MixType, MixUntilDissolved, and the container of the given sample.

Pattern Description: Greater than or equal to 1 minute and less than or equal to 72 hours or Null.

Programmatic Pattern: (RangeP[1*Minute, $MaxExperimentTime] | Automatic) | Null

Index Matches to: experiment samples

IncubationInstrument

The instrument used to perform the Mix and/or Incubation, prior to starting the experiment.

Default Value: Automatic

Default Calculation: Automatically resolves based on the options Mix, Temperature, MixType and container of the sample.

Pattern Description: An object of type or subtype Model[Instrument, Roller], Model[Instrument, OverheadStirrer], Model[Instrument, Vortex], Model[Instrument, Shaker], Model[Instrument, BottleRoller], Model[Instrument, Roller], Model[Instrument, Sonicator], Model[Instrument, HeatBlock], Model[Instrument, Homogenizer], Model[Instrument, Disruptor], Model[Instrument, Nutator], Model[Instrument, Thermocycler], Model[Instrument, EnvironmentalChamber], Model[Instrument, Pipette], Object[Instrument, Roller], Object[Instrument, OverheadStirrer], Object[Instrument, Vortex], Object[Instrument, Shaker], Object[Instrument, BottleRoller], Object[Instrument, Roller], Object[Instrument, Sonicator], Object[Instrument, HeatBlock], Object[Instrument, Homogenizer], Object[Instrument, Disruptor], Object[Instrument, Nutator], Object[Instrument, Thermocycler], Object[Instrument, EnvironmentalChamber], or Object[Instrument, Pipette] or Null.

Programmatic Pattern: (ObjectP[Join[MixInstrumentModels, MixInstrumentObjects]] | Automatic) | Null

Index Matches to: experiment samples

AnnealingTime

Minimum duration for which the SamplesIn should remain in the incubator allowing the system to settle to room temperature after the IncubationTime has passed but prior to starting the experiment.

Default Value: Automatic

Pattern Description: Greater than or equal to 0 minutes and less than or equal to 72 hours or Null.

Programmatic Pattern: (RangeP[0*Minute, $MaxExperimentTime] | Automatic) | Null

Index Matches to: experiment samples

IncubateAliquotContainer

The desired type of container that should be used to prepare and house the incubation samples which should be used in lieu of the SamplesIn for the experiment.

Default Value: Automatic

Pattern Description: An object of type or subtype Model[Container] or {Index, Container} or Null.

Programmatic Pattern: ((ObjectP[Model[Container]] | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic) | Null

Index Matches to: experiment samples

IncubateAliquotDestinationWell

The desired position in the corresponding IncubateAliquotContainer in which the aliquot samples will be placed.

Default Value: Automatic

Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.

Pattern Description: Any well from A1 to H12 or Null.

Programmatic Pattern: (WellPositionP | Automatic) | Null

Index Matches to: experiment samples

IncubateAliquot

The amount of each sample that should be transferred from the SamplesIn into the IncubateAliquotContainer when performing an aliquot before incubation.

Default Value: Automatic

Default Calculation: Automatically set as the smaller between the current sample volume and the maximum volume of the destination container.

Pattern Description: All or greater than or equal to 1 microliter and less than or equal to 20 liters or Null.

Programmatic Pattern: ((RangeP[1*Microliter, 20*Liter] | All) | Automatic) | Null

Index Matches to: experiment samples

Preparatory Centrifugation

Centrifuge

Indicates if the SamplesIn should be centrifuged prior to starting the experiment or any aliquoting. Sample Preparation occurs in the order of Incubation, Centrifugation, Filtration, and then Aliquoting (if specified).

Default Value: Automatic

Default Calculation: Resolves to True if any of the corresponding Centrifuge options are set. Otherwise, resolves to False.

Pattern Description: True or False.

Programmatic Pattern: BooleanP | Automatic

Index Matches to: experiment samples

CentrifugeInstrument

The centrifuge that will be used to spin the provided samples prior to starting the experiment.

Default Value: Automatic

Pattern Description: An object of type or subtype Model[Instrument, Centrifuge] or Object[Instrument, Centrifuge] or Null.

Programmatic Pattern: (ObjectP[{Model[Instrument, Centrifuge], Object[Instrument, Centrifuge]}] | Automatic) | Null

Index Matches to: experiment samples

CentrifugeIntensity

The rotational speed or the force that will be applied to the samples by centrifugation prior to starting the experiment.

Default Value: Automatic

Pattern Description: Greater than 0 revolutions per minute or greater than 0 standard accelerations due to gravity on the surface of the earth or Null.

Programmatic Pattern: ((GreaterP[0*RPM] | GreaterP[0*GravitationalAcceleration]) | Automatic) | Null

Index Matches to: experiment samples

CentrifugeTime

The amount of time for which the SamplesIn should be centrifuged prior to starting the experiment.

Default Value: Automatic

Pattern Description: Greater than 0 minutes or Null.

Programmatic Pattern: (GreaterP[0*Minute] | Automatic) | Null

Index Matches to: experiment samples

CentrifugeTemperature

The temperature at which the centrifuge chamber should be held while the samples are being centrifuged prior to starting the experiment.

Default Value: Automatic

Pattern Description: Ambient or greater than or equal to -10 degrees Celsius and less than or equal to 40 degrees Celsius or Null.

Programmatic Pattern: ((Ambient | RangeP[-10*Celsius, 40*Celsius]) | Automatic) | Null

Index Matches to: experiment samples

CentrifugeAliquotContainer

The desired type of container that should be used to prepare and house the centrifuge samples which should be used in lieu of the SamplesIn for the experiment.

Default Value: Automatic

Pattern Description: An object of type or subtype Model[Container] or {Index, Container} or Null.

Programmatic Pattern: ((ObjectP[Model[Container]] | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic) | Null

Index Matches to: experiment samples

CentrifugeAliquotDestinationWell

The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.

Default Value: Automatic

Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.

Pattern Description: Any well from A1 to H12 or Null.

Programmatic Pattern: (WellPositionP | Automatic) | Null

Index Matches to: experiment samples

CentrifugeAliquot

The amount of each sample that should be transferred from the SamplesIn into the CentrifugeAliquotContainer when performing an aliquot before centrifugation.

Default Value: Automatic

Default Calculation: Automatically set as the smaller between the current sample volume and the maximum volume of the destination container.

Pattern Description: All or greater than or equal to 1 microliter and less than or equal to 20 liters or Null.

Programmatic Pattern: ((RangeP[1*Microliter, 20*Liter] | All) | Automatic) | Null

Index Matches to: experiment samples

Preparatory Filtering

Filtration

Indicates if the SamplesIn should be filter prior to starting the experiment or any aliquoting. Sample Preparation occurs in the order of Incubation, Centrifugation, Filtration, and then Aliquoting (if specified).

Default Value: Automatic

Default Calculation: Resolves to True if any of the corresponding Filter options are set. Otherwise, resolves to False.

Pattern Description: True or False.

Programmatic Pattern: BooleanP | Automatic

Index Matches to: experiment samples

FiltrationType

The type of filtration method that should be used to perform the filtration.

Default Value: Automatic

Default Calculation: Will automatically resolve to a filtration type appropriate for the volume of sample being filtered.

Pattern Description: PeristalticPump, Centrifuge, Vacuum, Syringe, or AirPressure or Null.

Programmatic Pattern: (FiltrationTypeP | Automatic) | Null

Index Matches to: experiment samples

FilterInstrument

The instrument that should be used to perform the filtration.

Default Value: Automatic

Default Calculation: Will automatically resolved to an instrument appropriate for the filtration type.

Pattern Description: An object of type or subtype Model[Instrument, FilterBlock], Object[Instrument, FilterBlock], Model[Instrument, PeristalticPump], Object[Instrument, PeristalticPump], Model[Instrument, VacuumPump], Object[Instrument, VacuumPump], Model[Instrument, Centrifuge], Object[Instrument, Centrifuge], Model[Instrument, SyringePump], or Object[Instrument, SyringePump] or Null.

Programmatic Pattern: (ObjectP[{Model[Instrument, FilterBlock], Object[Instrument, FilterBlock], Model[Instrument, PeristalticPump], Object[Instrument, PeristalticPump], Model[Instrument, VacuumPump], Object[Instrument, VacuumPump], Model[Instrument, Centrifuge], Object[Instrument, Centrifuge], Model[Instrument, SyringePump], Object[Instrument, SyringePump]}] | Automatic) | Null

Index Matches to: experiment samples

Filter

The filter that should be used to remove impurities from the SamplesIn prior to starting the experiment.

Default Value: Automatic

Default Calculation: Will automatically resolve to a filter appropriate for the filtration type and instrument.

Pattern Description: An object of type or subtype Model[Container, Plate, Filter], Model[Container, Vessel, Filter], or Model[Item, Filter] or Null.

Programmatic Pattern: (ObjectP[{Model[Container, Plate, Filter], Model[Container, Vessel, Filter], Model[Item, Filter]}] | Automatic) | Null

Index Matches to: experiment samples

FilterMaterial

The membrane material of the filter that should be used to remove impurities from the SamplesIn prior to starting the experiment.

Default Value: Automatic

Default Calculation: Resolves to an appropriate filter material for the given sample is Filtration is set to True.

Pattern Description: Cellulose, Cotton, Polyethylene, Polypropylene, PTFE, Nylon, PES, PLUS, PVDF, GlassFiber, GHP, UHMWPE, EPDM, DuraporePVDF, GxF, ZebaDesaltingResin, NickelResin, Silica, or HLB or Null.

Programmatic Pattern: (FilterMembraneMaterialP | Automatic) | Null

Index Matches to: experiment samples

PrefilterMaterial

The material from which the prefilter filtration membrane should be made of to remove impurities from the SamplesIn prior to starting the experiment.

Default Value: Automatic

Default Calculation: By default, no prefiltration is performed on samples, even when Filter->True.

Programmatic Pattern: (FilterMembraneMaterialP | Automatic) | Null

Index Matches to: experiment samples

FilterPoreSize

The pore size of the filter that should be used when removing impurities from the SamplesIn prior to starting the experiment.

Default Value: Automatic

Default Calculation: Resolves to an appropriate filter pore size for the given sample is Filtration is set to True.

Pattern Description: 0.008 micrometers, 0.1 micrometers, 0.2 micrometers, 0.22 micrometers, 0.45 micrometers, 1. micrometer, 1.1 micrometers, 2.5 micrometers, 6. micrometers, 20. micrometers, 30. micrometers, or 100. micrometers or Null.

Programmatic Pattern: (FilterSizeP | Automatic) | Null

Index Matches to: experiment samples

PrefilterPoreSize

The pore size of the filter; all particles larger than this should be removed during the filtration.

Default Value: Automatic

Default Calculation: By default, no prefiltration is performed on samples, even when Filter->True.

Programmatic Pattern: (FilterSizeP | Automatic) | Null

Index Matches to: experiment samples

FilterSyringe

The syringe used to force that sample through a filter.

Default Value: Automatic

Default Calculation: Resolves to an syringe appropriate to the volume of sample being filtered, if Filtration is set to True.

Pattern Description: An object of type or subtype Model[Container, Syringe] or Object[Container, Syringe] or a prepared sample or Null.

Programmatic Pattern: ((ObjectP[{Model[Container, Syringe], Object[Container, Syringe]}] | _String) | Automatic) | Null

Index Matches to: experiment samples

FilterHousing

The filter housing that should be used to hold the filter membrane when filtration is performed using a standalone filter membrane.

Default Value: Automatic

Default Calculation: Resolve to an housing capable of holding the size of the membrane being used, if filter with Membrane FilterType is being used and Filtration is set to True.

Pattern Description: An object of type or subtype Model[Instrument, FilterHousing], Object[Instrument, FilterHousing], Model[Instrument, FilterBlock], or Object[Instrument, FilterBlock] or Null.

Programmatic Pattern: (ObjectP[{Model[Instrument, FilterHousing], Object[Instrument, FilterHousing], Model[Instrument, FilterBlock], Object[Instrument, FilterBlock]}] | Automatic) | Null

Index Matches to: experiment samples

FilterIntensity

The rotational speed or force at which the samples will be centrifuged during filtration.

Default Value: Automatic

Default Calculation: Will automatically resolve to 2000 GravitationalAcceleration if FiltrationType is Centrifuge and Filtration is True.

Pattern Description: Greater than 0 revolutions per minute or greater than 0 standard accelerations due to gravity on the surface of the earth or Null.

Programmatic Pattern: ((GreaterP[0*RPM] | GreaterP[0*GravitationalAcceleration]) | Automatic) | Null

Index Matches to: experiment samples

FilterTime

The amount of time for which the samples will be centrifuged during filtration.

Default Value: Automatic

Default Calculation: Will automatically resolve to 5 Minute if FiltrationType is Centrifuge and Filtration is True.

Pattern Description: Greater than 0 minutes or Null.

Programmatic Pattern: (GreaterP[0*Minute] | Automatic) | Null

Index Matches to: experiment samples

FilterTemperature

The temperature at which the centrifuge chamber will be held while the samples are being centrifuged during filtration.

Default Value: Automatic

Default Calculation: Will automatically resolve to 22 Celsius if FiltrationType is Centrifuge and Filtration is True.

Pattern Description: Greater than or equal to 4 degrees Celsius or Null.

Programmatic Pattern: ((Alternatives[GreaterEqualP[4*Celsius]]) | Automatic) | Null

Index Matches to: experiment samples

FilterContainerOut

The desired container filtered samples should be produced in or transferred into by the end of filtration, with indices indicating grouping of samples in the same plates, if desired.

Default Value: Automatic

Default Calculation: Automatically set as the PreferredContainer for the Volume of the sample. For plates, attempts to fill all wells of a single plate with the same model before using another one.

Pattern Description: An object of type or subtype Model[Container] or Object[Container] or a prepared sample or {Index, Container} or Null.

Programmatic Pattern: (((ObjectP[{Model[Container], Object[Container]}] | _String) | {GreaterEqualP[1, 1] | Automatic, (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic) | Null

Index Matches to: experiment samples

FilterAliquotDestinationWell

The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.

Default Value: Automatic

Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.

Pattern Description: Any well from A1 to H12 or Null.

Programmatic Pattern: (WellPositionP | Automatic) | Null

Index Matches to: experiment samples

FilterAliquotContainer

The desired type of container that should be used to prepare and house the filter samples which should be used in lieu of the SamplesIn for the experiment.

Default Value: Automatic

Pattern Description: An object of type or subtype Model[Container] or {Index, Container} or Null.

Programmatic Pattern: ((ObjectP[Model[Container]] | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | Automatic}) | Automatic) | Null

Index Matches to: experiment samples

FilterAliquot

The amount of each sample that should be transferred from the SamplesIn into the FilterAliquotContainer when performing an aliquot before filtration.

Default Value: Automatic

Default Calculation: Automatically set as the smaller between the current sample volume and the maximum volume of the destination container.

Pattern Description: All or greater than or equal to 1 microliter and less than or equal to 20 liters or Null.

Programmatic Pattern: ((RangeP[1*Microliter, 20*Liter] | All) | Automatic) | Null

Index Matches to: experiment samples

FilterSterile

Indicates if the filtration of the samples should be done in a sterile environment.

Default Value: Automatic

Default Calculation: Resolve to False if Filtration is indicated. If sterile filtration is desired, this option must manually be set to True.

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

Index Matches to: experiment samples

Aliquoting

Aliquot

Indicates if aliquots should be taken from the SamplesIn and transferred into new AliquotSamples used in lieu of the SamplesIn for the experiment. Note that if NumberOfReplicates is specified this indicates that the input samples will also be aliquoted that number of times. Note that Aliquoting (if specified) occurs after any Sample Preparation (if specified).

Default Value: Automatic

Pattern Description: True or False.

Programmatic Pattern: BooleanP | Automatic

Index Matches to: experiment samples

AliquotAmount

The amount of a sample that should be transferred from the input samples into aliquots.

Default Value: Automatic

Default Calculation: Automatically set as the smaller between the current sample volume and the maximum volume of the destination container if a liquid, or the current Mass or Count if a solid or counted item, respectively.

Pattern Description: All or Count or Count or Mass or Volume or Null.

Index Matches to: experiment samples

TargetConcentration

The desired final concentration of analyte in the AliquotSamples after dilution of aliquots of SamplesIn with the ConcentratedBuffer and BufferDiluent which should be used in lieu of the SamplesIn for the experiment.

Default Value: Automatic

Default Calculation: Automatically calculated based on aliquot and buffer volumes.

Pattern Description: Greater than 0 molar or greater than 0 grams per liter or Null.

Programmatic Pattern: ((GreaterP[0*Molar] | GreaterP[0*(Gram/Liter)]) | Automatic) | Null

Index Matches to: experiment samples

TargetConcentrationAnalyte

The substance whose final concentration is attained with the TargetConcentration option.

Default Value: Automatic

Default Calculation: Automatically set to the first value in the Analytes field of the input sample, or, if not populated, to the first analyte in the Composition field of the input sample, or if none exist, the first identity model of any kind in the Composition field.

Pattern Description: An object of type or subtype Model[Molecule], Model[Molecule, cDNA], Model[Molecule, Oligomer], Model[Molecule, Transcript], Model[Molecule, Protein], Model[Molecule, Protein, Antibody], Model[Molecule, Carbohydrate], Model[Molecule, Polymer], Model[Resin], Model[Resin, SolidPhaseSupport], Model[Lysate], Model[ProprietaryFormulation], Model[Virus], Model[Cell], Model[Cell, Mammalian], Model[Cell, Bacteria], Model[Cell, Yeast], Model[Tissue], Model[Material], or Model[Species] or Null.

Programmatic Pattern: (ObjectP[IdentityModelTypes] | Automatic) | Null

Index Matches to: experiment samples

AssayVolume

The desired total volume of the aliquoted sample plus dilution buffer.

Default Value: Automatic

Default Calculation: Automatically determined based on Volume and TargetConcentration option values.

Pattern Description: Greater than or equal to 1 microliter and less than or equal to 20 liters or Null.

Programmatic Pattern: (RangeP[1*Microliter, 20*Liter] | Automatic) | Null

Index Matches to: experiment samples

ConcentratedBuffer

The concentrated buffer which should be diluted by the BufferDilutionFactor in the final solution (i.e., the combination of the sample, ConcentratedBuffer, and BufferDiluent). The ConcentratedBuffer and BufferDiluent will be combined and then mixed with the sample, where the combined volume of these buffers is the difference between the AliquotAmount and the total AssayVolume.

Default Value: Automatic

Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.

Programmatic Pattern: ((ObjectP[{Model[Sample], Object[Sample]}] | _String) | Automatic) | Null

Index Matches to: experiment samples

BufferDilutionFactor

The dilution factor by which the concentrated buffer should be diluted in the final solution (i.e., the combination of the sample, ConcentratedBuffer, and BufferDiluent). The ConcentratedBuffer and BufferDiluent will be combined and then mixed with the sample, where the combined volume of these buffers is the difference between the AliquotAmount and the total AssayVolume.

Default Value: Automatic

Default Calculation: If ConcentratedBuffer is specified, automatically set to the ConcentratedBufferDilutionFactor of that sample; otherwise, set to Null.

Pattern Description: Greater than or equal to 1 or Null.

Programmatic Pattern: (GreaterEqualP[1] | Automatic) | Null

Index Matches to: experiment samples

BufferDiluent

The buffer used to dilute the aliquot sample such that ConcentratedBuffer is diluted by BufferDilutionFactor in the final solution. The ConcentratedBuffer and BufferDiluent will be combined and then mixed with the sample, where the combined volume of these buffers is the difference between the AliquotAmount and the total AssayVolume.

Default Value: Automatic

Default Calculation: Automatically resolves to Model[Sample, "Milli-Q water"] if ConcentratedBuffer is specified; otherwise, resolves to Null.

Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.

Programmatic Pattern: ((ObjectP[{Model[Sample], Object[Sample]}] | _String) | Automatic) | Null

Index Matches to: experiment samples

AssayBuffer

The buffer that should be added to any aliquots requiring dilution, where the volume of this buffer added is the difference between the AliquotAmount and the total AssayVolume.

Default Value: Automatic

Default Calculation: Automatically resolves to Model[Sample, "Milli-Q water"] if ConcentratedBuffer is not specified; otherwise, resolves to Null.

Pattern Description: An object of type or subtype Model[Sample] or Object[Sample] or a prepared sample or Null.

Programmatic Pattern: ((ObjectP[{Model[Sample], Object[Sample]}] | _String) | Automatic) | Null

Index Matches to: experiment samples

AliquotSampleStorageCondition

The non-default conditions under which any aliquot samples generated by this experiment should be stored after the protocol is completed.

Default Value: Automatic

Programmatic Pattern: ((SampleStorageTypeP | Disposal) | Automatic) | Null

Index Matches to: experiment samples

DestinationWell

The desired position in the corresponding AliquotContainer in which the aliquot samples will be placed.

Default Value: Automatic

Default Calculation: Automatically resolves to A1 in containers with only one position. For plates, fills wells in the order provided by the function AllWells.

Pattern Description: Any well from A1 to H12 or list of one or more any well from A1 to H12 or any well from A1 to H12 entries or Null.

Programmatic Pattern: ((WellPositionP | {((Automatic | Null) | WellPositionP)..}) | Automatic) | Null

AliquotContainer

The desired type of container that should be used to prepare and house the aliquot samples, with indices indicating grouping of samples in the same plates, if desired. This option will resolve to be the length of the SamplesIn * NumberOfReplicates.

Default Value: Automatic

Default Calculation: Automatically set as the PreferredContainer for the AssayVolume of the sample. For plates, attempts to fill all wells of a single plate with the same model before aliquoting into the next.

Pattern Description: An object of type or subtype Model[Container] or Object[Container] or a prepared sample or Automatic or Null or {Index, Container} or list of one or more an object of type or subtype Model[Container] or Object[Container] or a prepared sample or Automatic or Null entries or list of one or more Automatic or Null or {Index, Container} entries.

Programmatic Pattern: (((ObjectP[{Model[Container], Object[Container]}] | _String) | (Automatic | Null) | {GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | (Automatic | Null)} | {((ObjectP[{Model[Container], Object[Container]}] | _String) | (Automatic | Null))..} | {({GreaterEqualP[1, 1] | (Automatic | Null), (ObjectP[{Model[Container], Object[Container]}] | _String) | (Automatic | Null)} | (Automatic | Null))..}) | Automatic) | Null

AliquotPreparation

Indicates the desired scale at which liquid handling used to generate aliquots will occur.

Default Value: Automatic

Default Calculation: Automatic resolution will occur based on manipulation volumes and container types.

Pattern Description: Manual or Robotic or Null.

Programmatic Pattern: (PreparationMethodP | Automatic) | Null

ConsolidateAliquots

Indicates if identical aliquots should be prepared in the same container/position.

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

Protocol Options

Organizational Information

Template

A template protocol whose methodology should be reproduced in running this experiment. Option values will be inherited from the template protocol, but can be individually overridden by directly specifying values for those options to this Experiment function.

Default Value: Null

Pattern Description: An object of type or subtype Object[Protocol] or an object of type or subtype of Object[Protocol] with UnresolvedOptions, ResolvedOptions specified or Null.

Programmatic Pattern: (ObjectP[Object[Protocol]] | FieldReferenceP[Object[Protocol], {UnresolvedOptions, ResolvedOptions}]) | Null

Name

A object name which should be used to refer to the output object in lieu of an automatically generated ID number.

Default Value: Null

Pattern Description: A string or Null.

Programmatic Pattern: _String | Null

Post Experiment

MeasureWeight

Indicates if any solid samples that are modified in the course of the experiment should have their weights measured and updated after running the experiment. Please note that public samples are weighed regardless of the value of this option.

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

MeasureVolume

Indicates if any liquid samples that are modified in the course of the experiment should have their volumes measured and updated after running the experiment. Please note that public samples are volume measured regardless of the value of this option.

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

ImageSample

Indicates if any samples that are modified in the course of the experiment should be freshly imaged after running the experiment. Please note that public samples are imaged regardless of the value of this option.

Default Value: Automatic

Pattern Description: True or False or Null.

Programmatic Pattern: (BooleanP | Automatic) | Null

Example Calls

Basics

Obtain diffraction patterns of mySamples:

Additional Options

Obtain diffraction patterns of mySamples with a specified ExposureTime and DetectorDistance:

Obtain diffraction patterns of mySamples using a less intense X-ray beam than the default:

Obtain diffraction patterns of mySamples with a fixed detector at a specified position:

Obtain diffraction patterns of mySamples with a detector sweep from -20° to 60° 2θ in 10° increments:

Obtain diffraction patterns of mySamples with a with a fixed detector at a specified position, while changing the angle of the sample relative to the X-ray beam:

Image the SamplesIn before collecting diffraction patterns:

Preferred Input Containers

If the sample is to be transfered as a slurry, containers in which samples can be easily resuspended as a slurry for loading onto the Model[Container, Plate, "In Situ-1 Crystallization Plate"] are perferred.

Data Processing

Plot diffraction data or multiple sets of diffraction data on the same plot:

Identify peaks using AnalyzePeaks:

Warnings and Errors

Messages (20)

AliquotRequired (1)

If Aliquot resolves to True without any aliquot options being specified, throw a warning:

DeprecatedModels (1)

Throws an error if trying to run on samples with deprecated models:

DetectorAngleIncrementTooLarge (2)

DetectorAngleIncrement cannot be greater than the difference between MaxDetectorAngle and MinDetectorAngle:

The difference between MaxDetectorAngle and MinDetectorAngle cannot be less than the minimum DetectorAngleIncrement:

DetectorTooClose (1)

DetectorDistance may not be closer than is allowed by the specified angles:

DiscardedSamples (1)

Throws an error if trying to run on discarded samples:

DuplicateName (1)

Throws an error if trying set Name to the same as an existing protocol object:

FixedOptionsRequiredTogether (1)

FixedDetectorAngle cannot be set to Null while DetectorRotation -> Fixed:

FixedOptionsWhileSweeping (2)

FixedDetectorAngle may not be specified when DetectorRotation -> Sweeping:

MinOmegaAngle and MaxOmegaAngle must be Null if DetectorRotation -> Sweeping:

InputContainsTemporalLinks (1)

Throw a message if given a temporal link:

MinDetectorAngleAboveMax (1)

MinDetectorAngle cannot be greater than MaxDetectorAngle:

MinOmegaAboveMax (1)

MinOmegaAngle cannot be greater than MaxOmegaAngle:

OmegaAngleIncrementTooLarge (2)

OmegaAngleIncrement cannot be greater than the difference between MaxOmegaAngle and MinOmegaAngle:

The difference between MaxOmegaAngle and MinOmegaAngle cannot be less than the minimum OmegaAngleIncrement:

PowderXRDHighVolume (1)

If the volume of the sample or specified AssayVolume is greater than 100 uL, throw a warning:

PowderXRDTooManySamples (1)

Throws an error if trying to run on too many samples:

SpottingVolumeTooLarge (1)

If the SpottingVolume is greater than the AssayVolume for a given sample, throw an error:

SweepingOptionsRequiredTogether (1)

MinDetectorAngle, MaxDetectorAngle, and/or DetectorAngleIncrement cannot be set to Null while DetectorRotation -> Sweeping:

SweepingOptionsWhileFixed (1)

MinDetectorAngle, MaxDetectorAngle, and/or DetectorAngleIncrement may not be specified when DetectorRotation -> Fixed:

Possible Issues

Slurry fails to transport sample into well

During transfer of the sample, an insufficent amount of diffracting material is added to the well such that no diffraction peaks are observed when the well is analyzed. Ensure the slurry is sufficiently concentrated so that diffracting sample is present in the well. In the figure below, a well did not contain enough material to diffract and produced a diffractogram characteristic of transmission through an amorphous material (the well plate).

Last modified on Fri 6 Dec 2024 08:31:48