Molecules

The Molecules menu provides access to all the functionality to setup and modify molecules in the project, view the information about molecular structures, atom assignment status, isotope labelling and others.

Atom Browser

This option activates the Molecules: Atom Browser popup, which contains a table of all of the assignable atoms and atom groups for a specified molecule (chain). This table can display particular types of chemical element, specific residue types and various prochiral options.

The Molecules: Atom Browser is the primary means to assign resonances to specific atoms or atomic groups and is prompted from the Assignment: Assignment Panel popup.  The popup indicates whether an atom or atomic group has been assigned or not by changing the colour of the assigned atoms in the table.

Molecule Setup

Opens the Molecules: Molecule Setup popup. This popup is used to create molecule systems. Molecule systems contain all the information on the molecular structure, and are organised into chains, residues and atoms. It is the atoms that NMR resonances can be assigned to.

Although Analysis allows the definition of very complicated molecular systems, in most cases molecular systems can be easily created based on a polymer sequence, e.g. in the case of proteins.

Add Sequence

This menu option opens the {Add Sequence} tab of the Molecules: Molecule Setup popup. It is a shortcut that allows the user to quickly set up a molecular system for linear biological polymers, i.e. proteins, DNA, and RNA by entering a sequence of residues, or by reading a file containing the sequence.

Residue Information

Opens the Molecules: Residue Information popup. This popup displays information about specified residues in the molecular system. It contains a table that displays information of a specific residue type in the sequence with connected neighbours, and highlights the assigned residues. E.g. all information about the position, neighbours and assignment status of all Alanines can be displayed at once.

The popup also contains a basic structure viewer that shows the 3D structure of the residue type, and indicates any existing chemical shift assignments of the atoms.

Isotopomer Schemes

Opens the Molecules: Isotopomer Schemes popup. This popup provides information about common isotope labelling schemes, lists and displays the atoms that are replaced by NMR active isotopes for each labelling scheme. In addition, the user can create and modify isotope labelling schemes.