RMXML Schema

Elements Found in a FORMULATRIX XML Crystallization Screen

The following text describes the RMXML crystallization screen schema elements. The element hierarchy characterizes how elements are related to other elements. Indented elements are contained by the elements that appear above them.

screen

This is the primary element of this schema and denotes a crystallization screen. A screen contains one or more conditions and lists all the ingredients used in these conditions.

conditions

This element represents the crystallization conditions used in the screen. For more information please see condition element.

condition

This element represents a crystallization condition and holds the information about all the ingredients and stocks used in this condition.

conditionIngredient

This element represents one ingredient in the condition and stores the type, concentration and optionally the pH of the ingredient being used in the condition. In addition, it stores a local reference to the stock of the ingredient used represented by the element stockLocalID. In case the ingredient used is a multi vial buffer, it also stores a local reference to the stock supplying the high pH content of the ingredient. Both these references point to the stock elements in an Ingredient element of the same RMXML document. For more information see the stock element. The conditionIngredient contains the following sub elements.

type

Specifies the type that the ingredient is used as in the condition. The examples could be Salt, Buffer and Precipitant etc.

concentration

Specifies what concentration the ingredient is used at in the condition.

pH

Specifies, for buffer ingredients, what pH the ingredient is used at in the condition.

stockLocalID

Specifies which stock of the ingredient should be used in the condition. The stock with the matching localID in an Ingredient will be used.

highPHStockLocalID

This is an optional element and can be used to specify a second stock of the same ingredient at a higher pH value than the stock specified by stockLocalID. The two stocks then can be mixed to get an intermediate pH value for the ingredient. The pKa value (monoproticbuffers) or the data in the titrationTable (polyproticbuffers) can be used to calculate the ratio of the low pH stock and high pH stock required to get the desired pH for the buffer. See bufferDataelement for more information. Like stockLocalID, the high pH StockLocalID has to match with the localID of a stock in an ingredient.

ingredients

This element lists all the ingredients used in this screen irrespective of whether they are already present in the system or not. The ingredients not present in the system get imported and ingredients that are already present in the system are ignored. If an ingredient has been referenced in a screen condition but is not present in this section then the XML document is invalid.

ingredient

This element stores the information of an ingredient that participates in crystallization experiments. The ingredient contains the following sub elements.

name

Specifies the descriptive name of the ingredient. The maximum length of this element is 50 characters.

shortName

Specifies the short name of the ingredient. The maximum length of this element is 8 characters.

aliases

This element lists all the aliases used for the ingredient. This is an optional element.

alias

Specifies an alias for the ingredient. Alias is another name for the same ingredient. Ingredient name, ingredient short name, and aliases must all be unique for a given ingredient.

casNumbers

This element lists all the CAS Numbers for the ingredient. This is an optional element.

casNumber

Specifies a CAS Number for the ingredient. The list of CAS numbers must be unique for a given ingredient.

types

This element lists all the types the ingredient can be used as.

type

Specifies an ingredient type for example Salt, Buffer, Precipitant, Organic (non-volatile), Organic (volatile) and Polymer etc. The type “Buffer” is a special case having specific meaning to it. An ingredient with “Buffer” as one of its types is required to contain at least one stock with a valid pH value (between 1 and 14). If “Buffer” is the only type for the ingredient then all of its stocks are required to have valid pH values.

bufferData

Specifies the pKa or titration data of an ingredient. This information is used in the pH calculations. This is an optional element but is required for buffer ingredients. This element contains sub elements pKa and titrationTable. Only one of these elements is required for a given ingredient. The pKa value (monoproticbuffers) or the data in the titration Table (polyproticbuffers) can be used to calculate the ratio of the low pH stock and high pH stock required to get the desired pH for the buffer.

pKa

Specifies the pKa of the ingredient.

titrationTable

Provides a place to store titration data for buffer ingredients.

titrationPoint

Specifies an acid to base ratio to achieve a specific pH value for a buffer ingredient.

pH

Specifies the pH of the ingredient that is achieved at a specific acid to base ratio.

acidToBaseRatio

Specifies the acid to base ratio that produces a specific pH.

stocks

This element lists all the stocks of the ingredient

stock

This element represents the stock of an ingredient. It has following sub elements

localID

This element is used to assign a document wide unique number to the stock. The stockLocalID element in the conditionIngredient element refers to this unique number to specify which stock should be used.

stockConcentration

Specifies the concentration of the stock.

units

Specifies the concentration units of the stock for example M (Molar), %w/v (percent weight per volume) and %v/v (percent volume per volume) etc.

defaultLowConcentration

Specifies the default low concentration of the stock. This is used as the lowest concentration value while calculating a range of concentrations for a given stock while designing an experiment. This is an optional element.

defalutHighConcentration

Specifies the default high concentration of the stock. This is used as the highest concentration value while calculating a range of concentrations for a given stock while designing an experiment. This is an optional element.

useAsBuffer

Specifies whether the stock should be used as a buffer. A stock for which this flag is not set does not become available in an ingredient stocks list when this ingredient is being used as a buffer in a screen or an experiment.

pH

Specifies the pH of the stock. If an ingredient is used as a “Buffer” type the pH must be specified. If the ingredient is used as a type other than “Buffer” then the pH should not be specified.

Vendor Name

Specifies the stock vendor name. The maximum length of this element is 50 characters. This is an optional element.

Vendor Part Number

Specifies the vendor assigned part number for the stock. The maximum length of this element is 50 characters. This is an optional element.

Comments

Provides a place to supply comments about the stock. The maximum length of this element is 1024 characters. This is an optional element.

Importing Ingredients from an XML Crystallization Screen

While importing an ingredient to ROCK MAKER from an XML crystallization screen, its name, short name, all aliases, and all CAS numbers are searched for in the ingredients database, to avoid creating duplicate entries for ingredients. If a duplicate entry is detected during the import process, you can choose to either merge the new ingredient with the existing one, or save the new ingredient after changing the conflicting field. This keeps your database free of unnecessary duplicate entries.

Related Topics

• Importing, Merging, and Exporting Ingredients