Plates

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Plates in XtalBase are sets of wells consisting of a set of components in the reservoir and another set in the macromolecule solutions ('drops'). The components are chosen from the stocks database. For each plate the user decides what kinds of components (stock classes) shall be present in either reservoir or solution. Because in many cases the pH will be set before stocks are combined to reservoir or macromolecule solution there is a pH defined for each component and not just one for the whole reservoir or the macromolecule solution.

The plates lists lists all plates within the current project. The current project can be selected by the link at the top of the window. The table contains per-plate links to the summary, setup, scheme, observation, stock selection views.

view plates

Fields in the plates table

Key	Database field	Header	Description
NUMID	NUMID	NUMID	The numerical id.
ID	ID	Plate ID	The short name of the plate.
Barcode	BARCODE	Barcode	The barcode of the plate.
Owner	OWNER	Owner	The owner of the plate. Users can view and copy predefined plates, which are owned by the 'admin' user.
Dat	DAT	Last update	The date on which the plate was last changed.
Storage	STORAGE	Storage	The location of the plate.
Description	DESCRIPTION	Plate description	A short description of the plate.
SetupDat	SETUPDAT	Setup date	The date on which the plate was prepared.
ObsDates	OBSDATES	Observation dates	The dates on which observations were recorded. The number of observation dates is unlimited.
ObsComments	OBSCOMMENTS	Observation comments	This field contains comments with respect to the whole plate made on the respective observation date.
Project	PROJECT	Project	The project which the plate belongs to. A project comprises all plates that involve biomolecules with the same crystallization behaviour.
Method	METHOD	Method	The method of crystallization (sitting drop, hanging drop, liquid diffusion, microdialysis, microbatch, slow cooling).
ProtBatch	PROTBATCH	Protein batch	This fields describes the origin of the protein that is the date and number of protein batch used for this plate.
Temperature	TEMPERATURE	Temperature	The temperature at which the experiment is performed.
Width	WIDTH	Plate width	The width of the plate.
Height	HEIGHT	Plate height	The height of the plate.
ReservoirVolume	RESERVOIRVOLUME	Reservoir volume	This value is only relevant for vapour diffusion techniques.
DropsPerWell	DROPSPERWELL	Drops per well	The number of drops per well.
ResClasses	RESCLASSES	Reservoir component classes	The classes of the components in the reservoir resemble the classes, which stocks can be associated with. These are currently precipitant, buffer, salt, additive (3 instances), detergent, and protein.
SolClasses	SOLCLASSES	Solution component classes	The classes of the components in the macomolecule solution resemble the classes, which stocks can be associated with. These are currently precipitant, buffer, salt, additive (3 instances), detergent, and protein.
Stocks	STOCKS	Stocks	This field contains all stocks including their respective class, which shall be part of the stock pool used for the random selection of components.
Notes	NOTES	Notes	The notes field can be used for annotations pertaining to the current plate.
Share	SHARE	Shares	The Share field is used to give other users viewing or modifying rights for a certain object. Permissions can be given to specific users, to the group to which the object owner belongs to and to all users.
IScorePar	ISCOREPAR	I score parameter	This fields refers to the set of parameters, which were used to calculate I scores for this table.
IScoreDat	ISCOREDATE	I score date	The most recent date on which the iscore was calculated for the plate.

Actions in the plates table

Icon	Description
	display (and edit) the plate
	create a new plate
	copy the current plate
	resort the well definitions of the plate
	view plates
	delete the plate
	display (and edit) the pipetting scheme of this plate
	display (and edit) the setup of this plate
	display (and edit) the observations of this plate
	display (and edit) the selected stocks of this plate. This selection is used for the random selection of stocks
	display the plate import form
	export plate data
	export multiple plates
	transpose the plate cells
	update the plate

View standard plates

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The standard plate view lists a collection of plates that were imported from commercial sources. These plate definitions are ready to copy.

display/edit observations

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In this view the observations of all wells of the plate can be edited. The score options are defined according to a user-defined set of scores as defined in the scores view.

Click here to see the observations view of an example plate.

display/edit plate parameters

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In this view all plate related parameters can be edited. Editable parameters in this view are: the plate short name, a plate description, the project, the protein batch, the crystallization method, the temperature, the reservoir volume, the plate dimensions, the component classes of the reservoir and the solution. At the end of the window the number of successful and unsuccessful wells of this plate are listed in order of decreasing success (observed crystals).

Click here to see the summary view of an example plate.

display/edit stocks for random selections

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In this view the stocks for random selections of drop components are selected. The class membership of a stock is given by the specification in the stock edit view. In order to use a stock in a random selection a concentration range must be defined as well as a pH range in case the stock is used as buffer.

Click here to see the stock selection view of an example plate.

display/edit pipetting scheme

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In this view the well composition (components, the volumes of stock solutions to be added and pH's) is defined. The components classes correspond to the classes defined in the plate summary view. In order to simultaneously set components for some or all wells the wells can be selected and filled with help of the selector menu at the top of this window.

The components are chosen from the stocks list. If you want to define a new component:

check your stock list to see, if this stock is already defined. If you want to use this stock as for instance precipitant and the stock is not included in the precipitant selection list, the stock might not yet be marked as a possible precipitant. In this case edit the stock and check 'precipitant' in the classes field.
if you don't find the stock you want, check, whether there exists the corresponding compound in the compound list. If you have found a suitable compound, create a new stock of this compound by clicking on 'make stock'
if the compound you need does not exist yet, you need to create a new compound and then create a stock based on this compound.

Click here to see the pipetting scheme view of an example plate.

Scoring panel

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This panel gives you a choice against which group of data the drop compositions are scored and which I score levels are applied when components are selected by random.

Please consult the view stats help text for an explanation of how I scores are calculated.

The three choices for the source data are:

BMCD, that is all 3547 conditions of the BMCD database
all users: all data stored in the system (except for BMCD data)
project: all data within the project, which this plate belongs to.

Other parameters are:

min score: This is the minimum value of the I score required for the condition in order to be accepted in random selections.
safe score: This is the value above which the condition will always be accepted.

If the actual score is between the min score and the safe score then a random number between these two levels is generated. If the actual value is above this random number the condition is accepted otherwise rejected.

Component and pH selector panel

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This panel is used to enter components including the volumes of stock solutions to be added and pH's in multiple wells at once. All manipulations with help of this panel will only affect the cells marked with a checkmark.

The panel lists the component selectors in two sections, the reservoir section and the solution section. Each section contains a list of component classes (e.g. precipitant or buffer). The available classes for each section can be selected in the plate summary view. If no classes are selected for the reservoir or the solution then the respective section will not be visible.

In each class a component, its concentration and the pH can be chosen. The component lists consist of all stocks that are available for the corresponding class. For instance only those stocks are listed in the buffer class which have been assigned buffers in the stock definition.

For each class three links 'set', 'random', and 'clear' are available for the component and another three links 'set', 'random', and 'clear' for the pH's. 'set' will fill in the selected component or pH into the selected cells, 'random' will prepare the cells for a random selection and 'clear' will erase the component or pH in the respective class.

When 'vertical interpolation' or 'horizontal interpolation' is selected there will be two fields for the volume and two fields for the pH per class. Values in the selected cells will be interpolated between these two values.

display/edit concentrations

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In this view the reservoir and drop composition (components, their concentrations and pH's) is defined. The component classes correspond to the classes defined in the plate summary view. In order to simultaneously set components for some or all wells the wells can be selected and filled with help of the selector menu at the top of this window.

The components are chosen from the stocks list. If you want to define a new component:

check your stock list to see, if this stock is already defined. If you want to use this stock as for instance precipitant and the stock is not included in the precipitant selection list, the stock might not yet be marked as a possible precipitant. In this case edit the stock and check 'precipitant' in the classes field.
if you don't find the stock you want, check, whether there exists the corresponding compound in the compound list. If you have found a suitable compound, create a new stock of this compound by clicking on 'make stock'
if the compound you need does not exist yet, you need to create a new compound and then create a stock based on this compound.

Click here to see the setup view of an example plate.

Scoring panel

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BMCD, that is all 3547 conditions of the BMCD database
all users: all data stored in the system (except for BMCD data)
project: all data within the project, which this plate belongs to.

Other parameters are:

min score: This is the minimum value of the I score required for the condition in order to be accepted in random selections.
safe score: This is the value above which the condition will always be accepted.

Component and pH selector panel

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previous topic: Plates
next topic: Import plate

This panel is used to enter components including their concentrations and pH's in multiple wells at once. All manipulations with help of this panel will only affect the cells marked with a checkmark.

The panel lists the component selectors in two sections, the reservoir section and the solution section. Each section contains a list of component classes (e.g. precipitant or buffer). The available classes for each section can be selected in the plate summary view. If no classes are selected for the reservoir or the solution then the respective section will not be visible.

In each class a component, its concentration and the pH can be chosen. The component lists consist of all stocks that are available for the corresponding class. For instance only those stocks are listed in the buffer class which have been assigned buffers in the stock definition.

For each class three links 'set', 'random', and 'clear' are available for the component and another three links 'set', 'random', and 'clear' for the pH's. 'set' will fill in the selected component or pH into the selected cells, 'random' will prepare the cells for a random selection and 'clear' will erase the component or pH in the respective class.

When 'vertical interpolation' or 'horizontal interpolation' is selected there will be two fields for the concentration and two fields for the pH per class. Values in the selected cells will be interpolated between these two values.

Import plate

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With this facility plates data can be imported into XtalBase. The format of the text to submit in the form should be one of the following:

Hampton format:

First line: a string containing the word 'formulation'. Everything before this word will be the Name of the new plate.

Second (non-empty) line (the specification of component types):

{regnr}{tab}[{comp type}]{tab}[{comp type}] units{tab}{comp type}{tab}pH{tab}[{comp type}]{tab}[{comp type}] units{tab}{comp type}{tab}pH{tab}...

{comp type} should be replaced by for instance 'buffer'

all following lines:

{line nr}{tab}{conc}{tab}{unit}{tab}{component}{tab}{conc}{tab}{unit}{tab}{component}...

Example:
Hampton Research Crystal Screen formulation - Copyright 2001
Reagent number[Salt][Salt] unitsSalt[Buffer][Buffer] unitsBufferpH[Precipitant 1][Precipitant 1] unitsPrecipitant 1[Precipitant 2][Precipitant 2] unitsPrecipitant 2
10.02MCalcium chloride dihydrate0.1MSodium acetate trihydrate4.630%v/v2-methyl-2,4-pentanediol
+ 23 more lines ...

Jena Bioscience format:

First (non-empty) line (the specification of component types):

{Spec}{tab}{comp type}{tab}Unit{tab}Conc.{tab}{comp type}{tab}Unit{tab}Conc....

{comp type} should be replaced by for instance 'buffer'

all following lines:

{line nr}{tab}{conc}{tab}{unit}{tab}{component}{tab}{conc}{tab}{unit}{tab}{component}...

Example:
CS-121Precipitant 1UnitConc.Precipitant 2UnitConc.BufferUnitConc.pHAdditiveUnitConc.
A 1Ethylene Glycol% v/v25.00NoneNoneNone
+ 23 more lines ...

The following component types are recognized:
Precipitant 1
Precipitant 2
Salt
Salt 1
Salt 2
Buffer
Cryoprotectant

It is likely that the components are not recognized by the system. In this case you must create "translations" for the respective component. In case the import facility encounters and unknown component name it will look through all translations and try to find a string, which is associated with a registered stock. If there is a match, the component name found in the text to be imported will be translated to the respective stock. If there is no matching translation you must create a new translation, that is the original component name must be associated with a stock name. If there is no suitable stock available, a new compound must be created and from this compound a new stock.
If the stock is a buffer, the pH will be read from the input text, otherwise the pH will be ignored.

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