Molecules: Molecule Setup
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.Â
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.Â
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.Â
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.