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Select Atoms and Residues for Assignment
This popup window allows the user to view and select specific atom, atom set and residue entities from any of the molecular systems within the CCPN project. Most importantly this allow the user to perform resonance assignment, of the signal phenomena observed in NMR spectra, to particular atomic groups, thus labelling the origin of a resonance. In a similar manner, spin systems (groups of resonances from the same residue) may be linked to residues. In Analysis such atom and residue assignment may be performed in a specific way, i.e. choosing a particular atom in a particular residue within the sequence. However, this system also allows the user to select atoms and residues in order to specify the type of a resonance or spin system; to say what kind of atom or residue a resonance or spin system relates to without actually specifying which position in the molecular sequence. This type-only information is useful to reflect the current state of knowledge, particularly during early stages of assignment, without having to make notes outside of the CCPN system.
This system has a second important function, to show the user the current assignment state for the atoms of the selected chemical element types, molecular chain (and bearing in mind any shift list) selection. The cells within the table will show a darker colour if they carry a resonance assignment (irrespective of whether the resonance is associated with peaks) and thus the user can quickly get a visual appreciation of the parts of the molecular chain that have been assigned and those that have yet to be assigned
Atom Table
In order to use this system the user must ensure that the various options have been chosen appropriate to what they wish to view. Generally in the first “Atom Table” tab the user selects which molecular chain in the upper left pulldown men and click the “Elements” buttons to specify which kinds of atom will be visible at this time. Naturally the selection of chemical elements will reflect the kind of operation or assignment that is being performed at the time. Thus for example if the user is assigning a 15N HSQC NOESY experiment which shows only 15N and 1H resonances then only the [H] and [N] chemical element buttons need to be toggled on. If the user wants to reduce clutter and only look at a particular type of residue (amino acid, nucleotide, sugar) then the “Residue” pulldown can be used to display only a subset of the sequence. The adjacent “Nucleotides” option is only relevant for nucleic acids like DNA & RNA, and allow the user the option of showing each residue on a single line (long row), or have the sugar phosphate and aromatic bas components displayed independently on separate lines; minimising clutter and the need to scroll.
There are a few functions at the bottom of the first tab that control assignment and link to other kinds of data entity in the CCPN project. The [Show ...] buttons allow the user to get a separate table of either the spectrum peaks or resonance phenomena that have been associated with the atoms or resonances that have been selected in the table above. Specifically the Selected Peaks and Selected Resonances popups are opened. This is useful to navigate from the molecule based information display into the spectrum display and to understand the links throughout the project. The [Remove Atom Assignments] button does as the name suggests and disconnects any resonances assigned to the selected atoms from those atoms. This merely removes the specific atom information for those resonances, it does not affect the linking of the resonances to any peaks. Lastly the [Set Ring Flip Equivalency] button is used on the selected residue for the rare occasions that aromatic rings (in residues like Phe & Tyr) display two distinct resonances for atoms that in most circumstances are indistinguishable in NMR spectra, because they are in very rapid exchange due to rotation of the aromatic ring around an axis of symmetry. In essence this makes Phe & Thr HD*, CD, HE* and CE separate into HD1, HD2, CD1, CD2, HE1, HE2, CE1 & CE2 selections. This operation is reversible but will naturally loose fidelity of peak assignments if a peak is assigned to only one side of the ring.
Options
The second tab gives the user further control over how atom information is displayed in the main table. The upper “Prochirals” section allows the choice of how to display stereochemical information for atom sets that are often not distinguishable in stereospecific way in NMR spectra. For example a Ser residue has both HB2 and HB3 atoms in its side chain, but these can prochiral atoms cannot generally be distinguished from one another in NMR spectra. In such circumstances it is commonplace to use non-stereospecific assignment labels like “HBa” and “HBb” so that two different resonances, usually with different chemical shifts, can be identified in NMR spectra, without needing to specify any stereochemical information. In this example “HBa” and “HBb” resonance assignments will both be linked to both HB2 and HB3, but this is done in a way that is mutually exclusive; Analysis knows that one really only goes to HB2 and the other to HB3, whichever way round that may be. If the user has structural information that allows a proper determination of which resonance goes with which stereochemical location, then the “Stereospecific” option can be set. This would make Ser HB2 and HB3 available as separate options to “HBa” and “HBb” which come from the “Non-stereospecific” option. The “Ambiguous” option is something of a remnant and is generally only used for situations when the atoms in the stereo group have exactly the same chemical shift. For Ser HB2 & HB3 this would provide the “HB*” option in the main table, however this is really just a pseudonym; assigning to this actually assigns to both the stereospecific HB2 and HB3 at the same time (not HBa, HBb).
The “Assignment Status” selection allows the number of atom options displayed in the main table to be reduced by only showing specific cells based upon what kind of assignment the underlying atoms have. For example the “unassigned” option may be selected to view more easily what has yet to be assigned. The “Shift List” pulldown controls which atom options are darkened, indicating resonance assignments, based upon the experiments that those assignments are made to and which set of conditions (and thus shift list) those assignments relate. By default this option is set to “<Ignore>”, meaning that all resonance assignments are considered. Selecting a specific shift list will reduce the indication of assignment to only those peaks that use that shift list (via the experiment’s connection).
The lower “Isotope Labelling” section is used if the user has any experiments that were performed with selective spin-active isotope labelling, which would reduce the complement of atom sites that were deemed to be visible in spectra and thus available for assignment. Here, the user selects which type of isotope labelling scheme was used, and what level of isotopic incorporation (between 0,0 and 1.0) must be present for an atom site to be visible. Atom sites that are not deemed to be visible will not be displayed in the main sequence + atom table.
Tips and Caveats
At some stage in the future it is planned that the Atom Table will become (optionally) context sensitive to the kind of atoms that ought to be visible in the specific spectrum being assigned at the time. For example if an HNCA experiment is assigned then only the H, N & CA atom options cane be displayed.
Documentation missing
Chain: Select the molecular system & chain to show atoms for
Residue: Select the type of residue to display atoms for, defaults to all types
Nucleotides: Select how to display rows of base and sugar-phosphate atoms for DNA & RNA nucleotide residues
Elements: The selection of which chemical elements to display atoms for
Table 1 | |
# | Sequence number code |
Residue | Residue type code |
Set Ring Flip Equivalency: Toggle whether the symmetric aromatic ring of selected residue
flips quickly on the NMR timescale
Remove Atom Assignments: Remove all resonance assignments from the selected atoms
Show Peaks: Show a table of all peaks assigned to the selected atoms
Show Resonances: Show a table of all resonances assigned to the selected atoms
Documentation missing
Non-Stereospecific: Whether to show distinct but stereoscopically ambiguous assignment options.
For example you may not know if a Serine Hb is “Hb2” or “Hb3”
Stereospecific: Whether to show stereospecific atom options (IUPAC system) like Serine Hb2 & Hb3
Ambiguous: Whether to include multi-atom ambiguous options like Ser Hb*.
Methyl groups are not affected by this option unless the whole group is prochiral.
Any: Show all atom options irrespective of assignments
Assigned: Show only atom options which are assigned to NMR resonances
Unassigned: Show only atom options which have no resonance assignments
Tentative: Show only atom options that carry tentative resonance assignments
Shift List: Select a specific shift list to determine an atoms assignment status or “<ignore>” to use any
Isotope Labelling: Select which per-residue isotope labelling scheme/pattern to use
0.25: Specify what proportion of atoms must be isotopically labelled (spin active) to be considered as assignable