This popup allows the user to control the definitions of molecules in the project. New molecules can be created, and existing molecules modified and deleted. Note that the functionality in the various tabs works depends on settings in other tabs in this popup.

Chains

The {Chains} tab allows the user to create new chains from template molecules, and modify or delete  existing chains in the project. 

The Molecules: Molecule Setup popup (Chains).

Chains table

The table lists all the chains currently defined in the project.

Mol System

The name of the molecular system that the chain is defined in.

Chain Code

The chain code.

Molecule Template

The template molecule that the chain was created from.

Residues

The number of residues in the chain.

Chain Fragments

The number of chain fragments.

Molecular Types

Lists the type of the molecular chain, e.g. protein.

Details

The user can specify any details about the chain here.

Mol System for new chain

Specifies the molecular system that is to be used for creating a new chain. Molecular systems are defined in the {Mol systems} tab (see below).

Template for new chain

Specifies the molecular system that is to be used for creating a new chain. Template molecules are defined in the {Template Molecules} tab (see below).

Show Seq

Opens the {Sequences} tab of this popup (see below).

Delete Chain

Deletes the currently selected chain. A chain can only be deleted if it has not been used for any assignments.

Copy Chain

Makes a copy of the selected chain in the current molecular system. This option may be used to create oligomers where there are one or more chains with the same sequence. This is the same as creating a new chain using the same molecular template as the existing chain.

Add Sequence

Opens the {Add Sequence} tab of this popup (see below).

Edit Molecule Templates

Opens the {Template Molecules} tab of this popup (see below).

Make Chain From Template

Creates a new NMR assignable chain in the current molecular system using the template specified in the [Template for new chain] pulldown.

Chains table 2

This table shows the chain fragments of the chain selected in the Chains table.

#

The fragments serial number.

Mol Type

The molecule type of the fragment, e.g. protein.

Residues

The number of residues in the fragment.

Start Seq Number

The starting number of the sequence of the fragment. The user can edit the sequence start number for a chain fragment (the residues will be renumbered sequentially).

The numbering may not overlap with any other chain fragments. This renumbering involves setting the SeqCode value for the fragments residues. This does not affect the assignment to these residues. The connection of atoms to resonances and peaks remains unaltered, but the Analysis display will be updated to reflect the new residue label.

Modifying this number can take some time, since all objects (peaks, assignments etcetera) have to be modified in the project.

Linear Polymer?

Indicates whether the chain is a linear polymer.

Sequence

Shows the first part of the sequence of the fragment.

Mol Systems

The {Mol Systems} tab lists all the molecular systems defined in the project, and allows the user to create new and rename or delete existing molecular systems.

The Molecules: Molecule Setup popup (Mol Systems).

Mol Systems table

The table listing all the molecular systems.

Code

The code of the molecular system.

Name

The name of the molecular system.

Chains

Lists all the chains in the molecular system.

Molecules

Lists the molecules in the molecular system.

Mol Types

Lists the molecular types in the molecular system.

Structures

The number of structures associated with the molecular system.

Details

The user can specify any details about the molecular system here.

Add Mol System

Adds a new molecular system to the project.

Delete Mol System

Deletes the currently selected molecular system. A molecular system can be deleted only if it contains no molecules.

Sequences

The {Sequences} tab shows a list of the residues within a selected sequence in the project.

The Molecules: Molecule Setup popup (Sequences).

Molecule

Specifies the molecule for which the sequence is shown.

Sequences table

This table shows all the residues within a selected molecule and the residue specific information.

Seq Code

The sequence code of the residue in the sequence.

Ccp Code

The Ccp Code for the residue, which is the identifier for the type of residue. Until or unless the molecule has been used to make assignable chains, the type of residue may be changed. Changing the residue here will cause the descriptor to revert to the default type for the residue.

Descriptor & Sterochemistry

The column describes the protonation state descriptor for the template residue. If the molecule has no chains this may be modified to one of the predetermined values for the compound. For example the user can specify a Trp as being protonated or deprotonated at its He1 position.

Mol Type

The molecular type of the residue, e.g. protein.

Polymer Linking

Specifies the position of the residue within a connected series of polymer residues:

• • start

  • middle

  • end

This may be set to none if a residue is not part of a particular chain, for example a cofactor.

Linked Residues

Shows which residues are linked to the given residue.

Add Polymer

Opens the {Add Sequence} tab to allow a new polymer sequence to be added.

Copy Sequence

Copies the current sequence by opening the {Add Sequence} tab with the sequence predefined. 

Add Compound

Allows the user to add a new compound to the sequence through the {Small Compounds} tab.

Edit Links

Opens the {Links} tab that allows the user to edit the polymer links.

Lock/Unlock Molecule

Locks/Unlocks the selected molecule. A molecule cannot be unlocked when it contains assignments.

Template Molecules

The {Template Molecules} tab shows a list of the template molecules in the project. The template molecules are molecule objects that are used as templates within the project. Such molecule templates are used to specify the sequences of molecular chains. One molecule template can give rise to several chains if the chains are identical in sequence, i.e. form a homo-oligomer or represent folded and unfolded species.

The Molecules: Molecule Setup popup (Template Molecules).

Template Molecules table

The table lists all the template molecules in the project. Selecting a molecule will display the residues and details about the molecule in the lower tables.

Name

The name of the molecule template.

Long Name

An optional long name of the molecule template.

Mol Type

The type of molecule, e.g. protein.

Chains

Lists the chains in which the template molecule is used.

Common Names

.....

Keywords

.....

Functions

.....

Details

Allows the user to provide details for the given molecule.

Seq Details

Allows the user to provide sequence details for the given molecule.

Show Seq

Opens the {Sequences} tab with the details of the selected sequence displayed.

Add New Molecule

Creates a new molecule object.

Copy Molecule

Copies the selected molecule into a new molecule object.

Delete Molecule

Deletes the selected molecule object. Molecules may only be deleted if they do not have any chains currently associated with them, or when they are not locked.

Add Polymer Residues

Opens the {Add Sequences} tab to allow the user to add new polymer residues to the molecule. New residues can not be added when a molecule is finalised. 

Add Other Compound

Allows the user to add a new compound to the sequence through the {Small Compounds} tab.

Template Molecules table 2

This table provides and overview of the properties of the selected template molecule.

Links

The {Links} tab allows the user to edit links for residues in selected molecules.

The Molecules: Molecule Setup popup (Links).

Molecule

Specifies the molecule for which links can be edited. Allows the choice of a molecule from the current project for which template residues may be chosen.

Residue Type

Specifies the residue type for which links can be edited. Selects which residue type the source residue has, as determined by Ccp Code. If multiple residues of the same type are present the specific residue can be chosen from the [Source Residue] pulldown. Note that this two-level selection of residue type is necessary because a single list of all residues in a molecule may be larger than most screen sizes allow.

Source Residue

Allows the user to select which template residue of the specified type the table should display links or connections for.

Links table

This table contains the selected residues' links.

Source's Link

Displays the type of link from the source residue to the destination residue:

• • next

  • prev (previous)

Destination Residue

Specifies the destination residue, can be set to none.

Destination's Link

Displays the type of link from the destination's residue to the source residue:

• • next

  • prev (previous)

Add Sequence

The {Add Sequence} tab allows the user to add new polymer sequences to specified molecules and molecular systems in the project.

The Molecules: Molecule Setup popup (Add Sequence).

Polymer Type

Specifies the polymer type of the sequence added:

• • Protein

  • DNA

  • RNA

  • Carbohydrate

  • DNA/RNA mix

Start Number

Specifies the sequence start number.

Cyclic

Specifies whether the polymer is cyclic or not. When selected, the resulting cyclic polymers contain no start or end points (see the |Polymer Linking| column in {Sequences} tab).

Input Type

Specifies the input type of the residues. Automatically adapts the information in the Sequence Input area.

1-Letter

1 letter code, e.g. T for threonine.

3-Letter/Ccp

3 letter code, e.g. THR, Thr for threonine.

Destination Molecule

Specifies the destination molecule to which the sequence is added.

Destination Mol System

Specifies the destination molecule to which the sequence is added.

Ccp Codes

Allows the user to select a residue from a library of residues to append to the sequence input.

Append

Appends the residue selected in Ccp Codes to the sequence input.

Sequence Input

This is the text input field where the user can specify the sequence.

Add Sequence!

Adds the sequence given in the Sequence Input area to the specified molecule and molecular system.

Tidy

Cleans up the information in the Sequence Input area for more convenient display. In case the input cannot be recognised as a sequence, a Warning will be displayed.

Read File

Reads a sequence from a file through the Read sequence file popup, and displays the information in the Sequence Input area. Please note that any text file can be read, and no validation is performed on the content of the text file.

Clear

Clears all the information in the Sequence Input area.

Reverse Complement

Creates a reversely complementary sequence of the specified sequence (for DNA/RNA).

Small Compounds

The {Small Compounds} tab allows the user to add compounds to the molecular systems from a database of small molecule compounds.

The Molecules: Molecule Setup popup (Small Compounds).

chemCompView

This is the frame that displays the chemical structure of the selected compound, if coordinates are present.

Mol Type

Specifies the molecule type for which compounds are displayed in the Small Compounds table. Options are:

• • Protein

  • DNA

  • RNA

  • Nucleic Acid

  • Carbohydrate

  • Other

  • All

Small Compounds table

The table listing all the small compounds. The contents depends on the selection of the Mol Type parameter, and shows for each compound the:

• • Ccp Code

  • 3-Letter Code

  • Long name

Destination Molecule

Specifies the destination molecule to which the selected compound will be added.

Add Compound

Adds the selected compound top the destination molecule.